To Love is to Destroy (On Hiatus)
by 15millerj
Summary: Valentine escapes during the uprising with a pregnant Jocelyn and Jonathan When forced to flee for her life 2 years later she leaves both children to be raised at the hand of the monster Clary with both angel and demon blood is trained to fight 4 her fathers cause And in the search for the mortal cup struggles with the desire to do what she's always been taught or follow her heart
1. Chapter 1

_**IM baaack….. and still in college. I am slightly obsessed with Jonathan. I don't know why. I think he's an interesting character. So I decided to write about him. And how he would act if he grew up with Clary. I don't know how many chapters there will be or how long it will be but I've been really stressing lately. Maybe writing will help. IDK. Also this is short bc it's a prologue. I want them to be longer.**_

 _ **Here is the trailer I recently made:**_

youtu . be /RTDXz7-KOCQ

 **you have to put the spaces together because this website wont let me post it correctly. or just type in To love is to destroy in youtube. its the one by Jenna Miller**

 **Ch 1**

Jocelyn Morgenstern paced outside on the back porch. Through the window she could see her four-year-old son, Jonathan on the couch watching his two year old sister Clarissa draw in a coloring book. His eyes were fixed on Clary with a strange look on his face. She was the only thing he actually cared about and Jocelyn knew it. Jonathan was a quiet boy but his eyes spoke a thousand words.

Jocelyn looked back down at her phone to see the one message she'd been dreading. The unmarked number was that of Lucian Greymark's: Jocelyn's best friend and her husband's ex Parabatai. Ex, because her husband fed him to the wolves. Literally.

" _He knows."_ She didn't need the meaning spelled out to her. She knew. Jocelyn had been able to hide the fact that it had been she who'd turned Valentine into the Clave two and a half years ago. Valentine should've died in the Uprising. She'd warned them plenty ahead of time. But this was a fact: Valentine was a smart man. And although the Clave had been able to "believably to the shadow world" dismantle the Circle, Valentines followers, and make many arrests Valentine had escaped. And Jocelyn had been forced to follow him. If she had known she'd become pregnant a month earlier, she would've fled.

She'd been terrified that her daughter could've been born a monster like her son. Valentine had continued his experiments. For the duration of the pregnancy she'd been fed angel blood and she had been sure demon blood. But Clarissa had been born a happy normal red headed green-eyed child. She like to babble and giggle and play. She was the complete opposite of Jonathan who'd been born with a lot demon blood in his system.

Jocelyn took a deep breath and walked slowly back into the living room. Jonathan's eyes darted to hers for a mere second before looking back at Clary. _Don't show him that you're scared._ Jocelyn thought. _Jonathan will know._ She had to leave. But she couldn't take her daughter. Jonathan was too cautious of her. It was getting to the point where Jocelyn had to argue with him before feeding her. Even picking her up was causing a problem. Jonathan would demand to come and he was very in favor of his father. Valentine had a good hold on the four-year-old boy. Slowly she went to the closet and pulled out her purse. She turned towards her kids. Jonathan was watching her with narrowed eyes.

"Where are you going?" He asked with his high pitched baby voice. Jocelyn pursed her lips.

"Your father wants rotisserie chicken for dinner. I have to run to the store." She said trying not to play with her hands. "Can I trust you to watch your sister for an hour?" He scrunched up his face.

"I'm four." He questioned. Jocelyn smiled.

"And you're very smart and capable. Aren't you?" Jonathan nodded once.

"Can you watch your sister?"

"Yes." Jocelyn smiled and took her keys off of the key hook by the front door.

"Bye Mommy!" Clary called looking up and smiling. Jocelyn had to bite her lip.

"Bye sweetheart." Only after she shut the front door did she let out a deep breath. This was so wrong on so many levels. The only thing that kept her going was her knowing that Valentine would be back soon. They wouldn't be alone long.

Jocelyn got into her car. She couldn't cry yet. She pulled out her phone and hoped the man she was calling answered on the first try. The ringing stopped. "Magnus Bane?" She asked quietly.

"Yes?" The voice asked cautiously. "It's Jocelyn Morgenstern. I-I need your help." After turning off the phone she drove about a block and threw it out the window. Then she drove towards New York City.

Valentine knew something was off when he noticed Jocelyn's car missing from the driveway. He hated cars. He hated anything mundane but it was easier to use those things than to use portals and get caught by the clave. He needed to stay off the book.

He walked into the house. Jonathan was watching television. He didn't see Clarissa. "Jonathan," He said getting the attention of his son. Jon looked up from the violent tv show. "Where's Clarissa?" Jonathan looked towards the couch. Valentine rounded his chair and followed his gaze. She was asleep there, her face buried in a pillow and a blanket over her body. "Where's your mother?" He pushed his lips together.

"She said she went to the store for chicken." Valentine looked at the clock. It was nearing 8. "Two hours ago." Valentine closed his eyes and took a deep breath. She'd run. And left the children alone. Without feeding them.

He'd always assumed that Jocelyn had been the one to rat him out to the Clave. He'd let it go. Tried to play it nice. That was until one of his men working inside Idris had announced at the meeting he'd held today that is was in fact Jocelyn. Forty others now knew and Valentine was now forced to act. Otherwise he would've been showing weakness. He ran a hand through his blonde white hair, thinking.

"Jonathan I need you to go upstairs and pack." Jonathan raised his eyebrows, showing emotion for the first time all day.

"Father-" Valentine took the blanket off of Clary and picked her up.

"Daddy?" She mumbled, rubbing her eyes with one little fist. She rested her head on his shoulder. "Where Mommy?" Valentine didn't answer.

"Now Jonathan. There's a bag in your closet." He waited until Jonathan had disappeared on the second floor before following him up. He placed Clary in her crib. She watched him with half closed eyes as Valentine packed all of her things into a duffle bag.

"What doing?" She asked sleepily.

"packing." He answered. "We're leaving." The more he thought about his wife, the angrier he got and he didn't want to take out his frustrations on his little girl. He could do that with Jonathan later. He'd wanted to move back to Idris for some time. He already had a house too. He finished throwing Clary's things into the bag and left her in the crib to go back his own bag. He then came back in put both bags on his shoulders and picked up Clarissa.

"Jonathan!" Valentine barked. Jonathan peeked his head into the nursery. "Come here boy. Bring your bag." He did so quietly. Jonathan had so many questions running through his head but he knew better than to ask them. "Don't let go of my pants." Valentine twisted the ring on his finger and together they disappeared.


	2. Chapter 2

**2\. Growing Pains**

 **C: 7**

 **J: 9**

It was the middle of night and Jonathan was fast asleep. His stele lay next to him on the nightstand. It was peaceful. There was a knock at his door. He cracked an eye open. "What?" He groaned out. The door opened and his redheaded sister slipped in. He could hear her accelerated heart beat and her quick breath as she made her way to his bed.

"Jon?" She asked quietly. He could hear the strain in her voice. Jonathan lifted his head off the pillow. He could see the sweat on her forehead. "It's happening again." Jonathan sat up and lit the lamp next to his bed. Clary rested her head on the edge of his mattress.

"Get in." He said in a still groggy voice. Clary did as she was told. "1-10."

"5," She said through gritted teeth. "no, 6." Jonathan pulled her into him. She gripped his arm. "I was having a bad dream-ow- and I woke up with pain in my stomach." Jonathan rested his chin on the top of her head and listened as she struggled through the pain. She had demon blood in her system, not as much as Jonathan, but enough that the extra angel blood that she also had occasionally liked to 'fight' the demon blood. Clary had been five when the pain had started. There'd been screaming and tears. But Valentine didn't like crying and honestly neither did Jonathan. It showed weakness and although the pain was extraordinary in Clary's mind, she'd learned to tolerate it. She didn't cry but she couldn't hide the amount of pain she felt. Jonathan was good at helping her through it, not that he knew the truth.

"In through the nose-"

"-out through the mouth." Clary gritted out for him.

"That's right." He said in the voice he only used around his sister. It was softer and gentler. He didn't actually like that voice very much. Clary groaned. "Do you want to take a bath? Didn't that help last time?" Clary moved her head down into his chest so that her face looked down, which forced Jonathan to lift his own head.

"Hold me." His arm was starting to hurt but not so much that he couldn't handle it. He'd been whipped and that hurt way more than a seven year old squeezing his arm. He rested his hand on the center of her back.

"Swearing helps." Jonathan said half jokingly. She snorted. Five minutes later Clary conceded to the bath and Jonathan left her in his bed to go start it. When he came back, her butt was up in the air and her face was pressed into his pillow. "Come on," He said gently, taking her by the arm. "Do you need any help?" He whispered outside of the bathroom door. Clary shook her head and smiled. "There's a candle in there."

"Thanks Jon." Jonathan nodded. He waited until he heard the splash of the water before venturing back into his bedroom blowing out his candle and falling back to sleep.

"Jonathan." Valentine's cold voice cut through the quietness of the kitchen. Jonathan jutted his head to the side to look up at his father who sat at the island reading through one of his journals.

"I will be away for the weekend." Jonathan pursed his lips, his eyes sharpening. "I need you to train your sister while I'm gone." He looked towards the door. "Where is Clarissa?"

"Sleeping." He answered. "She was having pains again last night." Valentine tilted his head to the side.

"They're becoming more frequent." He scribbled something down in his journal.

"Are you going to visit Him?" Jonathan asked scrunching up his nose. Valentine paused for a moment.

"Jealous Jonathan?" He asked coolly. He stood up and headed towards the door. "It's unbecoming." Valentine knocked on Clarissa's door. When no one answered he walked in. She was curled in her bed, red hair splayed in every direction. He sat down on the edge of the bed and watched her quietly. She was going to grow up to look just like Jocelyn. He was terrified of that day. He brushed back a curl. She opened her eyes.

"Dad?" She groaned stretching. "Hi."

"Hi." Clary looked around the room.

"What time is it?" She asked.

"About 9. You slept in." Inside Clary started panicking but Valentine didn't seem angry. "You were sick last night." Clary nodded. "Is the pain worse or the same? Better?" Clary shook her head.

"About the same." She answered sitting up. Valentine kissed her forehead.

"I'll be gone all weekend. There's a list of chores in my study. Watch your brother." Clary smiled.

"Of course father." Valentine stood up and headed towards the door.

"And don't let him touch the birds." He was gone. And they had the weekend.

"Just throw the knife at the target." Jonathan sighed watching Clary carefully. He had his arms crossed.

"I don't like this." Jonathan sighed obnoxiously loud.

"It's not that hard."

"Why can't I just use a Seraph Blade?" She complained.

"Because you need to know how to use other weapons. Just throw it Clary." Clary huffed and took aim. The knife sailed past the target. "Again."

"Jon-" She whined.

"Look," He growled. "You hit the target once and we can have lunch. Okay?" Clary grudgingly agreed. Unfortunately, even with her most focused attempts, after thirty minutes she still hadn't hit the target. "Step over." Jonathan picked up three knives and threw each on in succession, each one hitting a major part of the body target. Clary rolled her eyes.

"Show off." She snapped turning to leave. Jonathan followed her.

"You're on chicken duty today." Jon said brushing past her. Clary tensed.

"You actually enjoy killing those chickens. Why don't you do it?" Jonathan sighed.

"Why are you so pissy today? Just do it." He walked into his fathers study and shut the door in her face. Jonathan was going to read books all day while she was forced to do all the chores. Clary went outside with gloves and chopped off one of the chicken's heads. She plucked the feathers and put it away for later. Then she cleaned out the pens and removed eggs before going inside to clean the kitchen and mop the floors. Jonathan came out around dinnertime. Clary hadn't started cooking yet.

"I'm not cooking dinner." Clary said matter-of-factly. Jonathan shrugged.

"I didn't ask you to." He said rolling his eyes. Clary left the kitchen and went outside near a maple tree. From there she watched the sky. It was a beautiful day and Clary itched to draw but Valentine didn't really approve of her hobbies. She had some paper and regular pencils but that was all he ever gave her. They distracted her from her training. After a while she sensed Jonathan near her. She hadn't heard him approach.

"Am I like you Jonathan?" She asked. He came to sit down next to her. They didn't look at each other.

"Father says I'm a monster." Jonathan answered after a while. "That no one but him will ever love me."

"I love you Jon." Clary said quietly. Jonathan didn't smile. He stared out at the hills in the distance.

"I don't think you always will Clary." He frowned. "I'm the reason mother left." He truly believed that. "She left us because she couldn't love a monster."

"Did Father tell you that?" Clary asked. Jonathan didn't answer. She didn't believe it for a second. "Do you remember her?" He finally looked at his sister.

"Yes." He said. "She was afraid of me." They sat there quietly together until the sun started to set. "The answer to your earlier question." He said as they walked back to the house, the sun setting behind them. "No, I don't think you're like me." Clary frowned. She wanted to be. She wanted to be as strong as her brother. She didn't want to be weak and sickly. If the pains continued her father wouldn't let her go on missions when she was older. She'd be stuck in the house doing chores. They were both only children. Clary seven. Jonathan nine. They had time to grow and change. They _had_ time. At least, that's what Clary kept telling herself.

The next day Clary and Jonathan spent the day sparring. Mostly it was just Clary watching while Jonathan beat up a punching bag. She wanted her father to be proud of her. Some day he would be. Valentine came back that evening. He greeted Clary with a kiss on the cheek but didn't near his son. Jonathan stood stock still as he eyed his father. "Jonathan." He said. "What havoc have you caused this weekend?" Clary didn't know what he was talking about. Jonathan had been with her the entire two days. The only time she hadn't seen him had been when he'd hid in the study and when they both had been sleeping. Jonathan didn't answer as Valentine walked around the children and set his bag on the table. "I trust you two had an eventful weekend." Jonathan's eyes seemed to darken as Valentine spoke. Clary wondered why. She smiled up at her father.

"Yes Dad." She answered. Valentine nodded.

"Good." He turned and disappeared into his study. Jonathan's expression hadn't changed.

"Are you okay?" Clary whispered. Jonathan's eye moved to hers but his body stayed still. His hands were clasped behind his back.

"Jonathan." Valentine reopened the door and stood there, arms crossed. "Would you come in here?" Although he phrased it as a question, it was not. He was angry. But trying to hide it from Clarissa. Nodding Jonathan walked past his father into the room. "Clarissa there's a new book in my bag for your studies. Why don't you take it to your room. Read the first two chapters and write down what you learned." Clary nodded.

"Sure Dad." Valentine closed the door.

Jonathan stood at attention as Valentine rounded on him. "I will give you a chance to explain, because that is the kind of man that I am." Jonathan only looked at him with hateful eyes, though his face was void of emotion. Valentine slapped him hard across the face. His head snapped painfully to the side and a red welt appeared on his cheek. Yet he still did not speak. "Jonathan Christopher." Nothing. Jonathan said absolutely nothing. "I was gone for two days. _Barely_ two days and you managed to rearrange my books, pour water on my work, hide my journals…" Valentine trailed off. Jonathan honestly did not care. Valentine knew that.

Muttering to himself he grabbed Jonathan painfully by the arm and yanked him into the hallway, through the house, and down to the basement. The basement was locked most of the time. Valentine didn't want Clary venturing down there. It was where he preformed most of his experiments. It was dark and dungy. He threw Jonathan at the cement wall. "Take off your shirt boy." He snapped. Jonathan did as he was told.

"Why do you visit him?" He snapped, throwing his shirt on the ground. "Why is he more important than us?" Valentine opened up a chest on the adjacent wall and pulled out a demon metal tipped whip.

"He is an experiment Jonathan." Valentine said calmly. "Just like you and your sister are." Jonathan crossed his arms over his small chest. "Turn around." Taking too long, Valentine turned Jonathan around himself. "Why can't you just do what you're told?" He snapped slicing the whip hard down Jonathan's back. Jonathan grunted. Valentine continued. After ten Jonathan cried out. He'd never gotten more than ten before. Jonathan was still a child and learning. But Valentine continued, on and on until Jonathan could no longer support himself and fell to his knees. He rested his head on the cool wall and sniffled. Trying not to cry. His breath came out in gasps as Valentine cleaned up and knelt beside him.

"You need to learn your place." Valentine said. "Every time I go out you do something reckless and stupid. That stupidity only hurts yourself." He stood and walked over to his table. There, he started working, leaving Jonathan on the floor.

Jonathan wiped the few tears that managed to escape, his eyes burning. "You love them more than me." He said after a few minutes of silence. "You named that boy Jonathan too, to replace me. And you show more affection for Clarissa." Valentine looked up at him. "I'm just your tool. I'm not your son." Valentine set his instrument down.

"You love Clarissa more than you love you, Jonathan." He said. "It's been obvious since the day she was born." Jonathan was quiet. "You sit there accusing me of hating you when I care for you the most." Jonathan scoffed. "The other boy is too soft. He's a good fighter but the extra angel blood in his system has made him incapable of killing when he sees it unnecessary. Clarissa is sick. She needs to be cared for-"

"You called her an experiment." Jonathan said quietly. "But she seems normal…"

"What do you know of normal Jonathan?" Valentine laughed. "You've never met anyone _normal."_

"Mother." He answered quickly. "She's like mother." Valentine looked down at his work. He wasn't denying it. "What's making her sick father?" Valentine had never explained the truth to Jonathan about his sister. Sure, he knew that he had demon blood in his system but he did not know that of Clary. Valentine continued working for a few minutes before answering.

"Before she was born, I fed her mother both angel blood and demon blood." He answered. "I figured it would be good to have a middle person: The other boy with Angel blood, you with Demon blood and Clary with both. I'm currently working on trying to figure out what's happening with her and how to stop it. I _believe_ that her extra angel blood is trying to get rid of the demon blood, which is what's causing her pains." Jonathan was silent. "Next time she gets sick, if it's at night, I want you to wake me. I need to get a sample of her blood." Valentine picked Jonathan up and set him on his feet. "Now get out. I have work to do."

Jonathan managed to make it up the steps and to his door without Clary seeing him. He probably looked disgusting. His hair was matted with sweat and black blood was trickling down his leg. He opened the door and froze. Clary sat on his bed, reading. She smiled when she saw him, unaware of the pain he was in or the punishment he'd just been dealt.

"What are you doing in here?" He snapped. Clary raised her eyebrows.

"I was worried about you." She answered. "Are you-"

"Get out." He growled. Clary jutted out her lip.

"Bu-"

"Get. Out." He didn't like to talk to her like this. He kept his back to the wall. She jumped off of his bed. She looked near to tears. "You're such a baby." He snapped. "Get out of my room and quit crying." She stopped at the door holding the large book to her chest.

"You're such an asshole sometimes Jonathan." His shoulders sagged as she slammed the door. He made his way to the shower and turned it on. As he stripped out of his ruined jeans and slipped into the hot water he gritted his teeth. Blood Pooled around his feet and washed down the drain. He could never understand Idris. How they didn't have electricity yet they had running water. It was a weird place. He sat down and let the water painfully hit his back. He could take this pain. That over the whip any day. His brain was still running and turning. He couldn't help but think about his earlier conversation with his sister. Currently, she acted sweet and innocent. But there was demon blood in her system. Maybe, sometime not so far off, Clarissa would turn out to be just like him. Maybe they were both monsters.


	3. Chapter 3

**3\. Growing Up**

 **C: 10**

 **J: 12**

 ** _Disclaimer: Don't own TMI. Wish I did. But I don't._**

 *****More reviews, more chapters*****

"Clary be careful." Jonathan called from the floor. He watched tensly as his little sister jumped from one beam to another. She was smiling. Happy. An emotion Jonathan didn't understand. In fact he didn't understand emotions at all. "Don't F-" Clary jumped and missed, catching herself with her hands, her head below the plank. Sighing Jonathan walked under her, fifteen feet below. "Drop." He said. "I'll catch you." He always did. But Clary, as stubborn as she was shook her head.

"I got this." She grunted as she heaved one arm up and tried to pull her body over the side.

"Don't push it." He called back. She did. And slipped. And fell right into Jonathan's arms. "I got you little sister." He smiled, setting her on the floor. She didn't try to stand. She hated drops like that as it made her dizzy. "You should be in bed." He said softly. She huffed.

"Exercise helps."

"No it does not." Valentine's voice boomed through the training room. Jonathan shot out of his crouch and stood at attention. "Clarissa you should be in bed." Clary looked at the floor. "Why don't you just listen?"

"Because," She answered softly "I don't want to be weak." _I want to be like Jonathan._ Valentine shook his head in annoyance. Clary's pains had gotten better, but she'd been having dizzy spells and fatigue and Valentine wanted her safe until those things passed.

"Jonathan, leave the room." Valentine ordered, refusing to look at his son.

"Yes sir." He said. Once the door had shut, Valentine spoke again, his voice softer.

"Are you hurt?" He asked kneeling in front of her. Clary shook her head.

"No. Jonathan was watching me."

"Good." He looked up at the beams that cris-crossed the ceiling. "You will be strong some day. And this won't be a problem." Clary's eyes lit up.

"Are you sure Father?" Valentine was fairly certain. The demon blood in her system seemed to be settling. She was getting a bit more snippy and argumentative at times like Jonathan but he was fairly certain it was just her growing up.

"You won't ever be like your brother." He said. "No matter how hard you train." Clary lowered her shoulders. "There's too much… darkness. Too much demon blood in him-"

"I have demon blood."

"You have _some._ Jonathan has a lot. You are not _part_ demon. Jonathan is. He will never have the kind of distractions nephillium do." Clary sighed. "You will do great things some day."

"I would do anything for you Dad." Valentine patted her head.

"I know."

Jonathan paced outside of the house. He was sure Valentine would come after him. He shouldn't have let Clary up on those beams. He should've made her stay with him and practice throwing. She was awful at that. Sure enough Valentine came outside a few short minutes later, his hands clasped neatly behind his back. He didn't appear to be angry.

"Jonathan." He said in greeting. Jonathan looked up at him.

"Father."

"You're hand in twitching." Jonathan hadn't noticed. He put his right hand in one of his pockets. He expected to be yelled at. But that didn't happen. Instead Valentine said, "Walk with me." Jonathan followed his father passed the chicken coop and the garden, towards the maple trees. He was quiet. "I have been thinking." Valentine said finally. "About your sister."

"What about her sir?" He asked.

"Her situation. How she's been sick. You know that I've been feeding her some of your blood." Jonathan tensed. He knew. It bothered him, but it had been making Clary better. "She's getting stronger. She's no longer fragile. I'm going to stop and see how she reacts. If it goes well, I'm going to be sending her away." _No._ Jonathan froze in his spot and Valentine had to turn back.

"Sh-she's only ten Father." Jonathan said quickly. "She- she needs us." _She needs me. I need her._ Valentine nodded.

"It will be a few more years Jonathan. But I need to find the Mortal Cup. I've always assumed that your mother had it. I still do and I need Clary to find it for me." Jonathan knew about the cup. "Clary will be going with her mother."

"You found her?" Valentine's eyes sharpened.

"I never _lost_ her Jonathan. She got the help of a warlock to hide her location. Her mistake was going to an institute where I had eyes."

"Sorry, I never meant to infer that." Jonathan said bowing his head.

"Accepted." They continued walking.

"Father?" Valentine looked down at him "What if Jocelyn doesn't have the Cup?" Valentine tilted his head to the side.

"Just trust me Jonathan."

"I do Father."

Jonathan knocked softly on Clary's door. He'd just finished one of his workouts with Valentine. There were bruises all over his arms and at the moment he couldn't find his stele. When she didn't answer he opened her door and stepped. She was sound asleep in the tangled black satin sheets, her hair splayed in every direction and her hands covered in Charcoal. Valentine had finally relented and bought her a few art supplies. It made her happier and Valentine actually liked when she smiled.

Jonathan found her stele on her dresser. He drew a quick Iratze on his skin. Jonathan slipped the sketchbook out from under her hand and smiled as he saw that it was a picture of himself. He set it on the nightstand and gently cleaned the smudge on her cheek.

"Jon?" She whispered, almost dreamlike.

"Shh," He said sweetly "Go back to sleep." One of her charcoaled hands wrapped around his sweaty one.

"Hold me?" He hesitated at the request. Clary was the only one who showed him any kind of affection. Valentine certainly never showed anything. He also knew that he had feelings for Clarissa that were anything but brotherly. If Clary ever knew she'd see him how Valentine saw him. A monster. His demon side called for her and it drove him insane. "I had a bad dream."

He lay next to her and pulled her into him. She smiled happily and snuggled into the warmth of his chest. Jonathan lay there tense for a few minutes trying to get himself under control. He wanted to keep her safe. He would always keep her safe. Even if Valentine took her away from him. The thought made him angry so he focused on the fruity smell of her hair.

"Jon?" She whispered.

"Yes Clary?"

"I love you." Jonathan didn't immediately respond. Why was it so hard for him? He knew that he wanted to protect her. He knew that he cared for her, but the word love… Sighing, he kissed her forehead and realized that he didn't actually have to say anything back, because she'd already fallen asleep.

 ** _A few weeks later_**

"Jon!" Clary snapped at him as she rubbed her sore ankle. "Why are you being so hard right now?" Jonathan rolled his eyes.

"You said that you wanted to get better." He answered. "You don't get stronger by going easy. Come on." She took his outstretched hand and got back on her feet. He threw her a seraph blade. "Come at me." Huffing she got into her stance blade raised. Their blades met in the air, unaware that Valentine had entered the room. He watched them as they ducked and rolled. Jonathan kicked Clary's legs out from under her and she managed to recover quickly. Valentine noticed that although Clary was a good fighter, she was robotic- too used to her sparring partner's moves to really develop her own. Valentine didn't really train with her. He'd have to start. Once Clary fell flat on her back and Jonathan decided to pin her Valentine decided to announce his presence.

"Children," He said in greeting, walking farther into the room. Jonathan stood up at attention, while Clary laid there lazily on her side looking at him.

"Hey Dad," She said breathing heavily.

"How are you feeling?" He asked, once again ignoring Jonathan. Clary shrugged.

"Not bad today. A little out of breath but that's probably because _Jonathan_ keeps acting like he's got some vendetta." Jonathan rolled his eyes.

"All I did was make it harder for you." He said. "Which is something you need if _you're going to get better."_ Valentine nodded.

"Your brother is right." Huffing Clary fell backward onto the floor and closed her eyes.

"Thanks." She said sarcastically. Jonathan shrugged.

"Just trying to help." Clary groaned.

"I want to see you two work with your opposite hands." Valentine said. Jonathan nodded. Clary muttered okay. They'd done it before. Not as often as they should but they had. It took two minutes for Clary's blade to be thrown across the room.

"I'm seeing spots." Clary said moving over to the bench. "Just give me a minute." Valentine sat down next to her.

"Jonathan, water." Nodding he grabbed the canteen on the floor and handed it to his sister. She drank it greedily. "You okay," She nodded slowly stood up. "good, I need you both to come downstairs with me." Clary tensed. She'd never been down there before. Jonathan looked over at her then back at Valentine.

"Father what-" He stopped as he and his father made eye contact. He immediately understood and a smile started to creep on his face.

"Clarissa needs to learn, Jonathan. It's important." Clary looked at her brother.

"What?" She asked quietly. No one answered her. Valentine unlocked the door to the basement. Jonathan walked down behind Clary so she would turn and run. Clary stilled when they got to the floor causing Jonathan to bump into her. He rested a hand on her shoulder. Valentine pulled up a chair from the side of the room and patted it.

"Clarissa, sit." Eyes slightly wide, she moved to sit down. In the center of the room, was a man and a woman. Both were in their late thirties, and both were hanging by their hands with rope. A gag was tied around their mouths.

"What did they do Father?" Jonathan asked like this was normal. Clary was still in shock. The two Shadowhunter's eyes darted back and forth.

"Oh, they gave away some valuable information to the Clave." He said. "They were _supposed_ to be getting _me_ intel, but… you get the rest."

"Punishment?" Valentine looked down at his twelve year old son. He did this at least once a month to keep the monster in him at bay. Before, he'd had to buy a new stock of chickens every few months. He'd come out, normally early and the morning, and find all ten of them dead.

"I was thinking slow death." Jonathan smirked. He didn't always kill people. If Valentine let him kill someone every month there'd be no one left. "I will be in my study. And Jonathan?"

"Yes Father?"

"One is for you. The other one is to teach Clarissa." Jonathan looked over at his nervous sister.

"Yes sir." Valentine left. Clary heard the door lock.

"Jon, what is this?" She asked softly. Jonathan opened up a drawer under the workbench and pulled out a smaller metal box.

"What? Are you scared?" He didn't ask it in a rude way. It was a simple question.

"No." She said. She really wasn't. She may have appeared scared from her facial expression, but it was really just shock. "I'm just… confused." Jonathan nodded.

"Come here."

"But father said-"

"Father left me in charge. Come here." Clary got up out of her seat. "Does this bother you Clary?" Was he asking if she found him a monster for liking this?

"No." Her genuine answer made him smile. He laid out his tools.

"Good." He reached up and untied the man's gag. He then picked up a large kitchen knife and studied the weight of it before looking up at the man's blue eyes. It must be terrifying to see a young twelve-year-old boy about to torture and kill you.

Clary stood in the shower staring down at her feet as blood swirled down the drain. It wasn't her blood. Jonathan had killed both the man and the woman. He'd told Clary that he took off the gags because he enjoyed their cries. He enjoyed the terror on their face, and he enjoyed watching the blood as it fell down their torn bodies. He liked it slow and he liked it bloody. It was something Clary felt that she should've hated. It was something that was morally wrong. But the truth was, that she'd enjoyed every second of it. Of Jonathan holding her hand as he guided down the woman's stomach. How he'd whisper specific gruesome instructions in her ear while holding the instruments. She'd enjoyed every _single_ second of it. And _that_ is what terrified her.

When she came out of the shower and back to her room, she found Jonathan sitting on her bed. Clary shook out her wet curly red hair. "Hi Jon." She said simply, pulling out some clothes from her dresser. She decided on a black shirt and yoga pants. Seeing as Jonathan wasn't moving to leave, and was currently being his creepy quiet self, she went into the bathroom and changed.

"I get to do that once a month." He said calmly. "But it was more fun with you there." Clary glanced at him as she opened her desk for her sketchbook.

"Yeah?" Jonathan hopped off of the bed.

"Yes." He leaned against her desk. "I hid it from you because I thought you'd find it revolting. I didn't even know Father-"

"Are you trying to defend what you were doing?" Clary asked picking up her pens. "Sit down." She said absently.

"I-"

"You don't need to." She sat on her bed. "Sit." With a questionable look on his face he slowly sat down in her desk chair.

"Why-"

"I want to draw you. Sit." He ran a hand over his face and sighed.

"O..kay." Clary looked at him and smiled.

"I like your confused look." She said. "I don't see it much."

 **Okay! A lot of things in this chapter. Maybe too many. I've rewritten this like three times… okay, so** ** _please please please_** **tell me what you think! AND I LOVE SUGGESTIONS! R &R!**


	4. Chapter 4

**3\. Secrets**

 **C: 14**

 **J: 16**

 _Jump. Duck. Kick. Roll._ Clary repeated in her head. _Go back. Go Forward. Do something different. Swing._ She was sweating. She was tired. She wanted water. But Valentine wouldn't relent. This was one of her last tests. In the last two years he'd taken it upon himself to train her. There was no more sparring with Jonathan. Both children worked with Valentine exclusively. If she failed, there'd be more of these… torturous hours. When they stepped through the training room doors, Valentine was no longer her father. He was her instructor and she had to do everything he said without question. He'd warned her beforehand that he would not go easy. She hadn't taken so literally until he'd slapped her two years ago. The first time in her life that he'd dared hit his daughter.

Valentine managed to grab her ponytail and pull it, catching her off guard. In response she lashed out her foot and pulled him down. Together they rolled on the floor. She managed to get her knee up to his stomach and she threw him to the side. A dizzy spell was starting, but Clary had to push threw it. He'd stopped letting her take breaks every time it happened. She stood up slowly and shook off the feeling and lunged for her Seraph Blade on the other end of the room. She grabbed it with her left hand as Valentine got hold of her foot. He yanked. She kicked out with her free foot and used her Blade to slice his wrist. Valentine let go and Clary struggled to get back on her feet. He'd popped her ankle out.

"Concede Clarissa?" He asked shaking off the blood rolling down his sleeve. Clary smiled.

"Nope." To finish she had to have him pinned with her blade pointed at his chest. Or a headlock, which is what she managed a minute later. She took a sip of the water from her canteen. "Father?" She asked. He looked at her. "May I…?" She asked pointing at her ankle and the hundreds of bruises covering her body. Valentine nodded.

"Yes." He said. Clary took out her stele and drew the Iratze. She took a seat on the bench. "You've improved." Valentine said sitting next to her. She brushed the sweat off of her face.

"I need a shower."

"You do." He agreed. "But after you run the perimeter." Clary widened her eyes. "You still have twenty minutes left in our time. We're going to use all of it." Clary nodded.

"Yes, Father." She sighed. He patted her leg and stood up.

"Good."

"You look awful." Jonathan said outside. Clary glowered at him.

"I haven't thrown up today." She said. "That's a plus. Jonathan nodded.

"That it is." Jonathan had grown to be six feet in height. Clarissa, at five feet had to look up at him to talk.

"I need to run. I'll talk to you later." Jonathan watched her as she jogged off to the edge of the property. He couldn't help but watch her lower half and smile. Shaking his head, he moved back into the house, and found his father in the kitchen drinking water.

"Jonathan." He said, "I need you to go on an errand."

"Yes sir."

"In London, there's a warlock. He goes by the name of Sam." Jonathan blinked.

"A warlock named Sam?" Valentine turned and walked towards the study.

"Yes." Jonathan followed him.

"Sam is a warlock?" Sighing Valentine spun back around at the door. He narrowed his eyes.

"Clarissa is the one that normally makes jokes." Jonathan shrugged.

"I'm not making a joke" Valentine opened the door. "Its just unusual that a warlock would go by something as mundane as Sam." Valentine groaned.

"You're going to London. Find Sam. He has a package for me."

"Yes sir."

"If he says he doesn't, he does." Valentine slipped the ring off of his finger and put it in Jonathan's hand. "I want you back for dinner."

"Yes sir."

Clary pulled her wet hair up into a ponytail and got dressed in clean clothes. Jonathan was gone for the rest of the day. It upset her. Valentine had been keeping them more and more apart. If she was free, Jonathan wasn't. If she was busy, Jonathan was free. It seemed the only time they had to spend with each other was at night when they were supposed to be sleeping.

Clary went down to the kitchen and sketched in her notebook until five. The guys expected her to cook dinner most nights. Unless Valentine came back with precooked meals, Clary spent a good two hours everyday cooking. Jonathan killed the chicken.

Jonathan came back at seven. Clary was just setting out the plates. "Are you okay?" She asked, noticing he appeared tired. He wore black tight clothes and held an old leather book in his right hand. His Seraph Blade was strapped to his side. His eyes darted to hers.

"Where's Father?" Rolling her eyes she nudged her head towards the study. Valentine was almost always in the study. Jonathan walked over, knocked once, and entered. Clary crossed her arms over her chest.

"A 'thanks' would be nice." She muttered. They were always hiding things from her. Clary sat down at the table and waited. They were _supposed_ to eat at seven. Valentine liked to have a strict schedule. She twirled her stele between her fingers in boredom. At 7:15 Clary moved to the island and opened her sketchbook. She just doodled, not really focusing on what she was actually doing. Finally at 7:30, her brother and father came out of the study. They were mumbling to eachother and the book Jonathan had earlier was gone. They sat down at the table without an explanation and started eating. After a minute Jonathan looked up.

"Foods cold." He said, though still eating it. Clary narrowed her eyes. Valentine looked between them.

"Oh, I'm sorry Jonathan." She snapped. "Would you like me to cook you a new plate?"

"Clarissa." Valentine said.

"Well, since you asked…" Clary tensed.

"Are you kidding me?" Jonathan did not joke. He made snide comments that may appear as jokes, but he did not joke. Clary shoved one more bite in her mouth before standing up with her plate and putting it in the sink.

"Clarissa." Valentine said again tersely. Clary ignored him.

"If you want a warm meal, eat when the food is ready." She snapped, heading towards the stairs.

"Clarissa." Valentine tried one more time. Once again she ignored him, and went up the steps to her room. Jonathan shoved another bite of the food in his mouth, as if nothing had happened. Valentine just stared at him. After dinner Jonathan cleaned the dishes.

"Is she in trouble?" Jonathan asked. "Because if that were me you'd have-"

"Jonathan?" Valentine sighed. "Shut up." He picked up Clary's sketchbook.

"I'm just saying." He put the last glass away. Valentine walked up to Clary's bedroom and knocked on the door before entering. She was sitting by the window, staring at the sky.

"You're thinking hard." Valentine said making Clary jump.

"Father," She said. "I'm sorry-"

"What are these?" He asked, handing her the black leather sketchbook. She looked up at him then down at the book before shrugging.

"Just doodles." She said. "I was waiting for you two to come out of the office.

"These aren't doodles." He said taking the book back and kneeling beside her. He flipped through the pages. Clary shrugged.

"I just draw those when I'm bored. I don't think they're actual runes." Valentine pulled Clary's stele out of her boot and handed it to her.

"Draw one." He said. Clary sighed.

"Dad…" Sighing she took her stele from him carefully. She looked carefully at her book. Valentine pointed to one.

"Just… draw it on the wall." Clary didn't think anything would happen. It was just a doodle. So she did as her father asked. At first nothing happened. It just sat there burned into the wood. But then, it started shining and Clary backed up into her father. The house shook slightly and a portal, an actual portal appeared. Clary gasped.

"Is that-"

"a portal." Valentine said smiling. "You made a rune for a portal." Clary gaped, and sat back down on the windowsill. Jonathan came into the room.

"Whats…" He stopped.

"The angel blood." Valentine muttered. He took her stele and cut through the rune, closing it. He handed it back to her. She was staring at the fading mark on the wall. He took the book back out of her hands and started flipping through them.

"We are trying all of these." He said. Clary paled.

"Father I-"

"Don't think I forgot about your behavior at dinner." She gulped. "Tomorrow?"

"Yes." He left out the door in a hurry, her sketchbook in hand. Jonathan stood there staring at her.

"What?" She snapped after a minute of staring.

"What's got you so wired up?" He asked.  
"Don't you have someone to kill?" Jonathan smiled.

"No, that's tomorrow." Flat. And truthful. "You made a portal." He said. Clary groaned.

"You sent Jonathan out again?" Clary asked the next day. Valentine nodded.

"He'll be gone the entire day?" Valentine looked up at her.

"Clarissa," He sighed. "Jonathan will not be here when you receive your punishment for yesterdays little outburst, nor will he ever know about it because for some reason he has this idea in his head that he has to _protect you._ " Clary looked away. "Now draw these runes." Clary had been whipped before. It had started a few a years ago, when Clary had started arguing with Valentine over her rigorous work out schedule. He'd waited until Jonathan had gone to bed, then made sure that he thought Clary was sick the next day so that she could get over the shock of it. Jonathan was just plain difficult when it came to Clary. "This has to be your angel blood." Valentine said after she'd finished. Clary stayed silent.

Sighing he stood up from his desk. "Come on." Clary followed him slowly down the basement steps. He went to grab the whip while she took off her top and leaned against the wall. He didn't do this often. Clary never screamed. Not once. She closed her eyes and pretended she was anywhere else. She bent her head as it hit her in the back. She grunted. After five Valentine stopped. "Draw an Iratze to stop the bleeding." He said.

"I know Father." She answered, grabbing her shirt.

"Go take a shower." Clary nodded.

"Yes sir."

It was late at night and Clary was just changing into her pajamas when her brother knocked on the door. She told him to hold on, and carefully pulled a loose black tank top over her head. The scars were still tender. She then opened the door.

"Hey Jon." She said as he walked passed her into the room.

"Clary." She shut her door softly. He sat down on her bed expectantly.

"I'm about to go to sleep." She said, rubbing one of her eyes.

"Okay," He answered.

"I… is it okay if I sleep alone Jon?" She wanted to lay on her stomach. When Jon slept over she had to sleep on her side, putting pressure on her back. Jonathan shrugged.

"I haven't seen you all day. I thought we could talk." Realizing he wasn't leaving any time soon, she moved to sit next to him on the edge of the bed.

"What about?" He was quiet for the longest time. Clary grew fidgety. "Jo-"

"I've been following Jocelyn." He said quickly, cutting her off. Clary stared at him. "Father told me to watch her. So I've been watching her." Clary stood up.

"I'm going to bed Jon." She said.

"Clary-" She looked at him.

"I'm going to bed." She wasn't mad. She didn't have any feelings towards it. But she was annoyed that it had taken him so long to tell her when she could've been cozy under her covers. Jonathan didn't budge from his spot.

"Clary-"

" _Jon."_ She moaned.

"There's something that I've been keeping from Father." Huffing she removed her hand from the lamp.

"Whatever you _think_ you're hiding from him, you're most likely not." Jonathan shook his head.

"Jocelyn has another kid." Clary blinked. "With a werewolf."

 **Um… yeah I just did that. It's my birthday everyone be nice :)**

 **Please give me suggestions.**

 **Reviews encourage me to post new chapters**


	5. Chapter 5

**5\. Change in the Weather**

 **C:14**

 **J: 16**

 ** _Cont._**

"You're lying." He had to be. There was no way that their mother, Jocelyn Fairchild, had _multiplied_ with a Downworlder.

"It's seven." Clary shook her head.

"Dad knows." Jonathan shook his head.

"I don't think he does." Clary laughed.

"He-he knows _everything_ Jonathan!" He stood and took both of Clary's hands in his.

"Clary, if Father knew, I don't think this _thing_ would still be alive." Clary looked into Jonathan's eyes. In truth, Valentine had been watching Jocelyn since she'd left him. However Jocelyn had hid the child inside the institute.

"You need to tell him." She said quietly. Jonathan shook his head.

"No. I do not." He said sharply. Clary's raised her eyes. "Clary he has a Circle member placed in that institute. If he didn't tell him I think there's a reason for that."

"He needs to know Jonathan." She was wide awake now and couldn't understand why Jonathan would hide this from Valentine. He had a right to know.

"I didn't tell you this so that you could run your mouth to Father." He snapped.

"Then why did you?" Silence. Jonathan turned away from her.

"I thought you had a right to know." He muttered heading towards the door.

"They're still married." Clary said. "Our mother and Father. He has a right to know." Jonathan stormed out of the room, leaving Clary once again alone in her bedroom. She wasn't going to be able to sleep. She probably lay in bed for thirty minutes before getting back up and going down to the kitchen. The house was quiet and Clary found herself slipping out the back door and into the cool spring air. She sat down on the back steps and stared up at the clear sky. The moon was a sharp crescent shape and stars glittered. It was going to be a long night.

 ** _2 months later_**

Jonathan stood quietly outside of the New York Institute. It was unusual that no one had come and gone in the three hours that he'd been watching. The werewolf usually left around this time. Another hour passed by, and still no one moved. "Jon," Clary said coming up from behind him. She held a cheeseburger in one hand and a Slurpee in another. "This stuff is amazing." This was the third time Clary had been sent with him to New York and the first time he'd let her go splurging. Every other time he'd forced her to stay by her side for eight hours. She had yet to see Jocelyn and that was because Jocelyn almost never left the institute. She was in hiding after all. "Jon, have you tried this?" Jonathan looked down at her.

"No." He said. She took a bite of the burger.

"Has he left yet?"

"No." Clary leaned against her brother and stared boringly at Institute. He subconsciously rested a hand on her opposite side. They were due back home soon but Jonathan relished this time away from Valentine. Valentine had his meetings in the house instead of traveling so he rarely left anymore. That forced Jonathan to stay in line.

"What are we waiting for?" She whispered. Jonathan didn't answer. Huffing, Clary moved out of her brother's arms and crunched up the foil that held the burger. "I'm thinking of trying French fries next." Jonathan rolled his eyes.

" _Clary._ " He groaned. She put her hands on her hips.

"What?" He shook his head.

"Lets go home." He said. Taking her stele out of her boot, she drew the portal rune on the brick wall of the ally and walked through appearing in front of the cottage. Jonathan followed shortly after. "Are you okay?"

"Leave me alone Jon." Clary said, heading straight for the stairs. There was absolutely no reason for Clary to be annoyed with her brother. None. So the fact that she was mad made no sense.

"Clarissa!" Valentine called as Clary's foot reached the last step. Jonathan stopped in the doorway. Valentine came into view from the kitchen. Grudgingly Clary made her way back down the steps and around to her Father. "Anything of interest?" Valentine was asking Jonathan. He shook his head. Valentine glanced at Clary who looked away. She didn't lie to her Father like Jonathan did. He knew that.

"No sign of Greymark." Jonathan said. "No one left the institute."

"Clarissa." Valentine said again. She noticed movement in his study. He had guests. "Will you come with me?" Jonathan tensed next to her. Without waiting for a response he turned and walked away, forcing Clary to follow. Inside, there was another man with dark hair and brown eyes. He moved to sit on the couch and picked up a journal. He didn't acknowledge her and Valentine didn't introduce him. Therefore, he was unimportant. "I have a job for you. You're first, and it's very _very_ important that you do this right." Clary smiled. She'd been waiting for this. "have you heard of the Mortal Cup?" Was this a joke?

"Yes sir." She answered. "It can make Mundanes into Shadowhunters." Valentine nodded.

"Among other things. I've been looking for it for quite some time and I believe that your mother has it." Clary held her breath. "And it's going to take you a while to retrieve it."

"How long is 'a while', father?" Valentine studied her.

"A few years." Clary's eyes widened. Jonathan had never been gone more than two days. "No one is going to trust you right away so I don't want you to start digging until about a year.'

"I'm sorry father." She said cutting him off. "Where are you sending me?"

"To live with your mother." Clary closed her eyes. "As I was saying, they won't trust you right away. So you'll stay there and be quiet and do as they say." She nodded. "There are also a few people you need to know. Maryse and Robert Lightwood used to be part of the Circle. They betrayed me for the Clave. They run the New York Institute. They have three children." He handed her a file. "Jace, as he goes by now, is the boy that I visited when you were younger." Hopefully Jonathan didn't know that.

"The one with angel blood."

"Yes. The other person is Hodge Starkweather. He is the man that I have on the inside. Do _not_ try and talk to him about your mission. Do not. Even if he stupidly approaches you. Play dumb, because he is an _idiot."_ Clary smiled.

"What of the child?' She asked. She'd ratted Jonathan the day after he'd told her about their sibling. Valentine had _not_ known and had decided not to tell Jonathan that he knew. Valentine worked his jaw.

"I'll let you know when I decide."

Jonathan was waiting in the kitchen when Clary finally emerged from the study. "Jonathan." Valentine said calmly.

"Father." Valentine looked back down at his daughter.

"Tomorrow night." He said, turning and walking back into the study.

"What-"

"Who's the guy in Father's office?" Clary asked, cutting off Jonathan.

"Blackthorn." He said. "Part of the Circle. What happened in there?" Clary walked passed him and up to her room. Jonathan followed.

"Father's making me go live with Jocelyn." Clary had never seen her brother freeze like he did right then. He appeared to almost stop breathing and his eyes grew hard. "Jon-" She went to touch his hand.

"No." He said so hard Clary backed up. "No way. You are not – no." Clary sighed, and threw the folder on her bed.

"Jon-"

"How long?"

"Jon-" He grabbed her arms.

"How long is he making you go there?"

"Two years at least." Jonathan shook his head and threw open her bedroom door to storm downstairs but Clary stopped him. "Jonathan stop it!" He spun back around and pushed her back into her room.

"Clary I need you. You don't- you don't get it." Clary shook her head. She didn't.

"Jon, I love you. And I'm not happy that I have to go. But I have to." Jonathan guided her until her back hit the wall. "I-it's going to be okay." She said softly. He was scaring her. Her brother rarely acted this way in front of her.

"You can't." Clary huffed. She had to crane her neck to look up at him as he was now towering over her. He had her blocked in with his arms. Clary tried to ignore it by fixing her brother's shirt.

"You need to be good while I'm gone." She said softly staring at his chest as she pulled down his white shirt.

" _Clary."_ He growled.

"Do as Father says. Don't fight with him. Don't argue."

 _"Clary."_

"Just listen to him. Please." She looked back up at his dark eyes. Before she had time to blink, with her hands still in his shirt, Jonathan dropped his head, his lips hitting hers with such force Clary couldn't pull away. She wanted to but with the state he was in she decided in that split second to let him have what he wanted. He'd had these feelings for her since she'd been little. As the years had gone on Clary had slowly caught on that Jonathan's feelings for her were more that just brotherly. He pulled away slowly. His hands went back to her arms.

"You can't go." He said softly. Clary looked away.

"Jon, I have to." It's easy to say he didn't take it well.

Clary didn't see Jonathan the next day, or when it was time to leave. She waited a good ten minutes after Valentine called for him but he never came down from his room. She didn't have anything on her except for her stele and a seraph blade clasped on her side. "If I need to contact you I'll be the one to do it. Don't try and contact me." Clary nodded. "This is important Clarissa."

"I know, Father." She held onto his arm as he twisted the ring on his finger. When they got to New York, Valentine turned on Clary and knocked her out with a hit to the back of the head. She hadn't expected it.

Clary woke up in a bed in a large room with eight other beds. She'd looked at pictures of the New York Institute the night before and came to realize that she was in the infirmary. And she wasn't alone. A girl, about Clary's age, stood off to the side watching her carefully. Clary groaned and stretched before sitting up slowly.

"Who are you?" The girl asked sitting on the opposite bed. Clary squinted.

"Where am I?" She asked, ignoring her. The girl raised her eyebrows.

"The New York Institute. You didn't come here on your own?" Clary shook her head.

"I was taking a walk on the other side of the city." She said. "I got knocked in the head." The girl stared at her.

"My brother found you outside on the steps." The girl said. "I'm Isabelle." She stretched her hand out.

"Clary." She didn't take the outstretched hand. "I shouldn't be here." She moved to get up but the girl Isabelle stopped her.

"I don't think you realize how serious your injuries were." She said quickly. Clary had never had much contact with anyone other than her brother and father. She wasn't very good at conversation. "You had two broken bones, your head was bleeding, and you had bruises everywhere." The double door entrance to the infirmary opened and a redheaded woman came into the room. Clary gulped. It was her mother. The woman stopped when she realized her daughter was awake. Clary's eyes hardened.

"Clarissa?" Jocelyn asked after a moment of silence. Clary didn't answer. She just glared at the shocked woman. Isabelle looked between them.

"Jocelyn? What's going on?" She asked. Jocelyn looked at her.

"Get in contact with your parents." She said. "They're going to want to be here." Isabelle gave Clary one last look before walking quickly, in very high heels Clary noticed, out the door. She was fourteen years old and wearing high heels. Clary looked back at her mother. "What are you doing here?" Jocelyn asked, unsmiling. Clary worked her jaw.

"I could ask you the same thing." She snapped. Jocelyn sat down on the farthest bed, respecting Clary's space.

"Clarissa-"

"Don't call me that." Jocelyn stared at her.

"What are you doing in New York?" She asked. "Did your Father-"

"My _father_ has no idea where I am." She continued snapping. "I ran away a few months ago." Jocelyn seemed weary.

"I'm sorry if I don't believe you." She said. "But Valentine is a very hard man to disappear from."

"You did it pretty easily." _She thinks._ Jocelyn stared at her. "I only left my brother. You left a husband and two kids."

"How is Jonathan?" Clary narrowed her eyes.

"You don't deserve to know how my brother is." She said. Jocelyn sighed.

"Claris-"

"Do. Not. Call. Me. That." She hissed. "Father called me that. Don't call me that." Jocelyn's face softened.

"What should I call you then?" She asked.

"Clary." She answered. Jocelyn smiled. That was the nickname she'd given her as a baby.

"Why did you run away Clary?" She could tell Jocelyn was pretending to believe her story.

"I couldn't stand him." She answered. "And… he hurt me." Jocelyn stood and moved towards her. Clary tried to move away, but her bed was against a wall.

"How did he hurt you?" Clary didn't answer. She looked away. Jocelyn sat down where Isabelle had been sitting. Realizing she wasn't leaving, Clary turned and pulled her black tank top off, revealing the whip scars. She heard Jocelyn gasp.

"Jonathan's worse." She said looking away.

"Clary…" The words died in her throat. "Why would he…"

"Punishment." She said. "For not listening." Jocelyn stood up quickly.

"I-I'll be back. Don't move."

Valentine slapped Jonathan across the face. "When I call for you, you come." He hissed. "I don't give a _crap_ what you're up to. You. Come." Jonathan's eyes hardened.

"You sent Clary away." He said. Valentine hit him again.

"Yes. Because I needed too. Don't be such a child." Jonathan kept his face neutral.

"She-"

"She what?" Valentine snapped. "I told you about this years ago. You had two _years_ to get over this!" He pushed him against the door of his bedroom.

"She keeps my… other side under control." He answered.

"What? The side that likes to kill? Jonathan, get over yourself!" Jonathan closed his eyes. Valentine slapped him one more time. "If you _ever_ do that again…" He trailed off, letting the threat hang. Valentine threw open Jonathan's bedroom door and stormed out leaving him there alone.

Jonathan would try and visit her. He had her portal rune. Hopefully he could do it without Valentine finding out.

He wiped the blood dripping from the corner of his mouth and sighed. He'd scared her the other night. That was why he hadn't gone down. He'd let his anger get the better of him and he'd _kissed her._ Jonathan turned and punched the wall, making a hole. What was wrong with him?

 **Ok. Done. I won't be updating for a few days. I have a ton of stuff due this week. I hope to have something up by Friday or Saturday.**

 **PLEASE: SUGGESTIONS! And review. Reviews keep me writing! If there isn't much interest, I'll stop writing. :(**

 **Thanks guys!**

 **-Jenna**


	6. Chapter 6

**Suggestions welcome!**

 **R &R**

 **-Jen**

 **6\. New Surroundings**

 **C:14**

 **J:16**

 ** _Cont._**

Clary paced the infirmary. It had been at least an hour since Jocelyn had left. When the doors finally did open Clary had about had it. She wasn't used to sitting still. She always had a job and was expected to complete it in a timely manner. She was so close to breaking the glass window.

It wasn't Jocelyn who came back in though. It was man about Jonathan's age with black hair and blue eyes. A Lightwood. He set a tray on the bed. "I brought you some food." He said. "A grilled cheese, I think. My sister doesn't know how to cook." Clary forced a smile. She had no idea what a 'Grilled Cheese' was. "I'm Alec, by the way." Clary leaned against the mosaic window with he arms crossed.

"Clary." She said in greeting. She did not like the vibe she was getting off of him. He was talking nice, but his body posture told her he was ready for her to attack.

"What are you doing here, Clary?" They'd sent him in to see if she gave different stories. Clary pushed off the window. Her black combat boots echoed as she approached him.

"Oh, you know. My Father's just a raving lunatic." Alec waited. "You know, Valentine Morgenstern?" Alec didn't say anything. Clary sighed. "Look, I was on the other side of the city and got knocked in the back of the head. Then I woke up here." Alec didn't seem to believe her. "I slipped away from my father about a month ago. I've been on the run since then." Alec shook his head.

"Here's the problem with that." He said. "Valentine Morgenstern is a very powerful man. You're a _child._ The chance that he doesn't know where you are is little to none." Clary crossed her arms over her chest. "And _if_ you were 'on the run' you'd be much more alert when walking out on the dark streets and you would most likely be able to spot someone before they were able to knock you in the head." Clary sniffed the burned sandwich and put it back on the plate. She went for the water instead.

"I can explain it to Jocelyn." She answered. Alec shrugged.

"Suite yourself." He turned towards the door. Alec Lightwood was going to be a problem. Jocelyn came back in a moment later.

"You wanted to see me?" Her voice was soft. She was trying to be nice.

"Do they know?" Clary asked leaning forward. Jocelyn sat down across from her.

"Know about what?" She answered.

"Father's experiments." Jocelyn tensed, answering her question. They did not. "I can… do things." She said. "I can create runes."

"Create runes?" She repeated slowly. Clary nodded. She pulled her stele out of her boot and drew a rune in the air, creating a portal. Jocelyn shot up.

" _That's_ how I got away from Father." Clary said after she closed it. Jocelyn seemed to pale.

"I can't believe…" She took another step back. "Were you looking for me?" She asked. Clary didn't answer. "Claris-"

"No." She snapped. "You left me with him. It's your fault all of this happened to me. Why would I go looking for _you?"_ Jocelyn looked down.

"I'm sorry Clary." She said. "I know you don't understand…" She trailed off. "When Maryse and Robert get here, I'll try and get you a room."

"I don't want to be here." She said. Jocelyn smiled as she walked towards the door.

"If you didn't want to be here, why didn't you create a portal and leave?" Clary was silent. They were Clary's puppets and all she had to do now, was pull the strings.

 ** _five days later_**

Clary was hiding in her room. Again. She didn't like eating with those people, especially since all they seemed to eat was takeout. They had that huge kitchen and no one cooked real food. Well, Jocelyn did, but it was for breakfast or lunch. Clary'd also learned that her other sibling was a girl. She'd managed to avoid the child so far mostly by avoiding meals but that was about to change.

Clary sat by the window of her large room and sketched a portrait of Jonathan. She liked her old room, where she was actually able to curl up into the window. Here, she had to drag a chair over. There was a knock at the door and Clary wasn't in the mood to stand and open it. She didn't have to anyway, because the person on the other end didn't wait long.

"Hi." He said, coming into the room. Clary looked up at him and knew immediately that this was the other boy that Valentine had raised. There was no way he was a lightwood as he had blonde hair and his eyes were a bright hazel color. "Uh, Jocelyn asked me to bring you down for dinner." He said. _Too soft._ That's why Valentine had sent the boy away. At least, that's what he'd told Jonathan. And the boy had no idea that it had _been_ Valentine to raise him.

"What's on the menu?" She asked absentmindedly, working on her brother's jawbone.

"Takis." He said.

"What? Is that some kind of vomit?" The name sounded gross on its own. The boy snorted.

"Pizza." He paused. "I'm Jace, by the way."

"I'll pass on the fast food." She said, expecting Jace to leave. He didn't.

"Jocelyn told me to tell you that if you don't come down to eat, you aren't getting anything." Clary shrugged. "What do you eat?"

"Not fast food." Other than burgers and slushies. Jace moved closer.

"What're you drawing?" Clary snapped the book closed and stood up. "Don't tell me. You need a nude model. I'm not in the mood but you could always ask Hodge. I hear he'll do anything for a -"

"Do you ever hear yourself speak?" Clary said, tilting her head to the side. Jace smiled.

"It's the best part of my day." Shaking her head, she moved passed him and into the hall. He followed close behind. "The kitchen is to the right down the steps." She didn't walk the Institute by herself. If she was out, someone had eyes on her. That's one of the reasons she'd hid in her room. She stopped at the entrance to the kitchen. The growing noise dropped to zero when they laid eyes on her.

Maryse and Robert, who Clary'd met only once were back in Alicante. Jocelyn seemed to run things. Isabelle sat at the end of a long table. Jocelyn stood by the counter with the two boxes. It smelled like grease. Clary's eyes met Alec's narrowed ones. Jace stepped passed Clary. "Alec, It's a girl." Jace said. "Surely you've seen girls before. Your sister Isabelle is one." Alec looked up at Jace and appeared to smile slightly, making Clary raise her eyebrows.

"Shut up Jace." He said, obviously not mad.

"Clary." Jocelyn said. "We've got food over here." Clary looked carefully around the kitchen. Anything to get out of eating that gross, greasy hunk of grease.

"Do you have any fruit?" She asked. Blinking, Jocelyn nodded.

"There are apples in the fridge." Jocelyn pulled out a red one for her and tossed it. Clary caught it easily with one hand and moved to sit down. She watched as they chewed their grease.

"Mom, where's your phone?" Clary didn't know what to expect when she saw her sister. She looked almost identical to Clary, with her bright orange hair and green eyes. The only difference was obviously the age, and the fact that the girl's hair was straight. Clary tried not to stare at the girl in front of her, despite the fact that the girl was staring at her.

"It should be on my desk." Jocelyn said. "Come, get some pizza." The girl drew her attention to the boxes and moved to grab a slice. She sat down across from Clary. Everyone seemed to be holding his or her breath. Clary shot the girl a glare and she immediately adverted her eyes.

"When's Max coming back?" She asked.

"Mom thinks he's safer in Alicante." Alec said. "It could be a while." The girl pouted her lip.

"What about Dad?"

"He's taking care of his pack." She said. "It could be a few days." Isabelle smiled.

"I could take you shopping tomorrow. If Jocelyn's okay with it." Clary glanced up at her mother. She seemed to be chewing her lip.

"it's been getting bad out there." She said quietly. "I'm not sure it's a good idea."

"The extra demonic activity has been at night mom." The girl whined.

"That's not what I'm worried about." Isabelle frowned.

"I think she'll be fine." She said. "Jace can come with us." Jace groaned. Clary, realizing she could earn some trust here spoke up.

"If you're worried about my father, he's not going to be out." All eyes turned on her. "He's in a different time zone. He'll be sleeping, not that he leaves the house anyway." That part was a lie. Valentine left constantly for meetings. Jocelyn folded her hands in front of her.

"I'm not comfortable with it." Everyone seemed to go back to his or her previous conversation. Except for Alec, who was staring at everyone with wide eyes, which landed on Clary. She responded by mouthing _what._

"Do none of you realize that she knows where Valentine Morgenstern lives?" Jocelyn sighed.

"Alec," She started.

"She knows things and you all are treating her like a guest." Clary stood up, half eaten apple in hand.

"Alec, calm down." Jace said.

"Do you trust her?" Alec asked.

"No." He said honestly.

"then sh-"

"Boys." Jocelyn snapped. "We are not having this conversation here." Clary continued into the hallway with her apple. No one followed her, unusually, so after standing there a while she decided to walk around. She'd never gotten a tour.

The first place she found was the library. Large, intricately carved wooden doors opened to a two-floor library, with books lining two of the fifty-foot walls. Jonathan loved books. At the end of the library was a short set of steps that led to a sub floor. A piano was pushed against the wall of stained-glass.

She could hear papers rustling somewhere in the room but couldn't see where it came from. She moved her fingers along the covers, trying to decipher some of the foreign words.

"Some of those are mid 18th century." A voice boomed. Clary spun around. Leaning against the second floor was an elderly man with greying hair. He walked down the spiral staircase and over to her. She waited patiently. "You must be Clarissa." He said, holding out his hand. Clary took it. "Hodge Starkweather." Clary smiled.

"Nice to meet you." She said.

"You like books?" he asked, turning away. _Interesting man._

"My brother reads more than I do." She answered honestly. "But I've been known to read one or two." He smiled.

"How many languages do you know?"

"three or four." Hodge nodded in interest.

"Clary." She turned to see Jace approaching her. "I'm sorry about Alec." Clary gave him a look.

"Why are you sorry?" She asked. "You're not Alec." Jace watched her move down the wall. "And anyway, he's right." Hodge moved away, but was clearly listening. This was good actually.

"Clary-"

"I do know where my father lives. Or where he lived. I've been gone a month. He's probably moved on by now."

"He was wrong to do that in front of your sister. Jocelyn's been trying to keep her out of this stuff. Sure, she knows who Valentine is, but that's about it." Clary turned on him suddenly.

"She's not my sister." She snapped. "I have a brother. I do not have a sister." Jace didn't respond. "Why haven't I been questioned?"

"Jocelyn didn't want to involve the Clave."

"Why?" Jace ran a hand through his hair.

"Do you have anyone you need dead?" Jonathan asked abruptly, making Valentine pause his work and look up at his son. Jonathan's entire body was tense, and he felt like he would snap any minute. He needed to get out and do something. He hadn't left the house in days.

"No." Valentine said after a good minute of staring, before going back to his work.

"Father I-"

"You can leave." Clary was what held him steady. When he felt like this, he usually went to her and watched do whatever it was she was doing; drawing, sleeping, anything. That safety was gone.

"Father." Sighing Valentine set down his papers.

"What do you want Jonathan?" He sighed. _Clary._ "I'm a very busy man." Jonathan closed his eyes. His hands were clenched at his side. Was it hot in here? Huffing Valentine stood up and grabbed Jonathan by the arm. He opened the basement door, unlocked, and pulled Jonathan down the steps. He opened up a door on the side and pulled Jonathan in. "Stay." He ordered, shutting the door in Jonathan's face and locking it from the other side. Jonathan called this room the _box._ That was because he couldn't hear or see anything. And because it was technically a box. Jonathan liked the dark. He liked the quiet… unless screaming was involved. When Valentine couldn't control him he put Jonathan in the box and let him cool off. He could hit the wall as much as he wanted. He could yell as much as he wanted, but he couldn't leave until Valentine let him out.

Jonathan punched the wall. He didn't feel his skin splitting open. He sat down on the hard floor and meditated. This was going to be a long day.

 **Okay, nothing** ** _awesome_** **in this chapter. You just met some more people.** **J**

 **Suggestions please!**

 **And reviews keep me posting new chapters. R &R**

 **-Jen**


	7. Chapter 7

**Baby Biscuit (Guest): I. Am. Laughing. So. Hard. Right. Now. Mostly because I had this chapter almost finished and I just read your review.** **J**

 **THIS IS WHY I LOVE REVIEWS**

 **-Jen**

 **C. 7**

 **C: 14**

 **J: 16**

 ** _Cont._**

 ** _Two Months later_**

Clary sat curled up on the couch in the library, sketching runes absentmindedly. She was bored out of her mind. Jocelyn wouldn't let her in the training room without Jace or Alec. If she was in the library, someone had to be with her. Pretty much anywhere she went she had to have an escort. Currently Jace was playing some medley on the piano. Clary couldn't help but watch him over her sketchbook.

She'd come to the conclusion that Jace was attractive. The only other young guy she'd ever really known was her brother. And he was her _brother_ so he didn't count. She'd also come to the conclusion that Jace and Alec were Parabatai. But Alec looked at Jace the way Jonathan looked at her. It wasn't brotherly. Jace was clueless to the fact.

"What are you playing?" Clary asked, setting her sketchbook on the couch and walking over to Jace. Izzy had given her some clothes. Though somewhat revealing, Clary was comfortable in them. They were dark and skin tight. And they worked with her favorite pair of combat boots that she happened to be wearing.

"River Flows in You." He said absently, hitting the keys softly. Clary leaned against the piano and watched.

"How'd you learn to play?" Jace closed his eyes, listening to his music.

"My father." He said. "When I saw him." He slowed the keys. "We had a piano in our home. He'd bring me a new book every time he came back. This is one of my favorites." She felt bad for him. He had this picture perfect idea of his father, and it was a lie.

"What happened to him?" Jace stopped playing and closed the piano.

"Died." He said sharply.

"I'm sorry if I upset you." She said honestly. Jace shook his head.

"No." He said. "I just don't think about him often. The Lightwoods are my family now. They have been since I was ten." He stretched back his arms. "Do you want to spar?" He asked abruptly. Clary raised her eyebrows. She'd never actually sparred with anyone here. They seemed to let her do her own thing.

"Aren't afraid to get beat by a girl?" She asked smiling slightly. Jace snorted.

"Me? Get beat by a… hah." Rolling her eyes she picked up her sketchbook and followed him out of the library, the melody he'd been playing only moments earlier stuck in the back of her mind. She hadn't known that her father could play the piano. He couldn't of taught Jace how without knowing.

The training room in the institute was four times larger than Clary's back home. It had more equipment than she'd ever seen. "Hand to hand, or blades?" She asked, throwing her book on the floor next to the door and removing her black leather jacket. Jace turned to look at her.

"Hand to hand work for you?" In other words, they didn't want her touching the blades. Nodding, she walked over to the padded floor. This would be fun.

"Give up?" Clary asked five minutes later, holding Jace's arms in a lock behind his head. He struggled for another minute before Clary released him. Alec had silently entered sometime during the sparring and approached them as Jace rubbed his arm. "Bruised your ego?" She asked. Jace laughed.

"No." He lied.

"Are you okay Jace?" Alec asked. Clary resisted the urge to roll her eyes. Jace waved him away. "You could've hurt him." Jace rolled his eyes this time, Clary noticed.

"Hardly." She snapped back.

"Alec, we were just sparring. It was my idea. Calm down." Alec didn't seem to like this answer but didn't say anything. "We need a rematch. Tomorrow?" Clary smiled.

"You're on." She said, moving off of the mats. Jace left the room and Clary moved to follow but Alec stopped her with his hands.

"You need to stay away from Jace." He said in her ear. Clary started laughing. Once again, she was being told to stay away from a Jonathan Christopher. The only difference was that this wasn't her father. He wouldn't hit her. "I'm serious. You're not good for him. You're going to _hurt_ him." Boy was he right about that. Clary lost her smile and pushed passed Alec.

"You're pathetic." She said, feeling a bit of darkness pulling at the words. She was still part demon. It did affect her when she got angry.

"How so?" Alec said back. Clary bent down and picked up her book.

"You act like you're the bravest in your little group." She snapped, standing upright and turning on him. "But the truth is you're the most afraid. You're feelings are getting in the way of your judgment."

"My feelings?" He laughed. Clary went to open the door to the hallway, but Alec slammed it back shut.

 _"Okay then."_ She mouthed with an annoyed look on her face. She turned on him and looked up. She hated being short. "Why don't you just admit it Alec." She said smoothly. She'd seen her brother angry. This was nothing compared to that. And she just enjoyed pissing people off. "You're in love with Jace." Alec straightened, like he'd been shocked. "You're in _love with Jace."_  
"We're-"

"What?" She snapped. "Brothers? Parabatai? - yes I have seen the runes. I know a thing or two about secret obsessions." Alec surprised her by grabbing her throat and lifting her into the wall. Her sketchbook fell to the ground.

"Say that again." He hissed into her ear. "And I. Will. Kill. You." Clary swung her leg up and kicked him in the stomach, forcing him to let go of her. She dropped hard to the floor, grabbed her sketchbook and bolted from the room. It wasn't that she didn't want to kick his ass, because she really did, but it would not make her father happy. Her demon blood was screaming at her to go back in there and finish the job. She needed to cool off. So when she got into her room and locked the door, she went into the bathroom. With the lights off, she got undressed and turned on the shower. Cold water should do the trick. And it did. After a few minutes, she felt her pulse slowing to a normal rhythm and her brain started working properly again. She got out, wrapped a blue towel around her waist and opened the door. When she stepped into her bedroom, she immediately noticed that she wasn't alone.

Spinning towards the bed she noticed a white haired man laying there. She tensed. He was going through her sketchbook.

"You must really miss me little sister." Jonathan said with a grin. Clary didn't smile.

"Does Father know you're here?" She whispered storming over to him. She could feel his eyes roaming her body.

"If I lied and said yes would that make you feel better?" Clary didn't answer.

"You need to leave." Jonathan frowned.

"Aren't you happy to see me?" He asked. She shook her head in annoyance and moved to her dresser.

"You didn't say goodbye." She said back. "Father called for you and you never came down."

"So you're mad at me." It wasn't a question. "Clary, you know I… handle things differently than you." She huffed and pulled out a black tank and some jeans. "I've watched you almost every night from my spot on the street, making sure you're okay. I've been _there_ for you." He'd moved off the bed and behind her while he talked. She looked up at the mirror connected to the dresser and he brushed one of her wet curls behind her ear.

"Jonathan," She whispered.

"I'll always be there for you." He said looking down at her. She stared at him in the mirror. Clary closed her eyes.

"How did you get in here?" She asked, her voice still soft.

"I have father's ring." He said.

"Good." She said. The portal rune tended to make buildings shake. "You can't do this again."

"I needed to see you." He said. Clary closed her eyes.

"I could be with someone. If they see you this whole thing is over. Father will kill you." Jonathan's eyes darkened.

"I'd like to see him try." There was a knock at her door and the handle turned. However, she'd locked the door. Clary spun on Jonathan and kissed him on the cheek.

"Go. Please." Jonathan kissed her on her forehead before twisting the ring on his finger and disappearing without another word. She took a deep breath and headed to the door.

"What?" She snapped and was surprised when she saw that it was her little sister.

"Were you talking to someone?" She asked looking passed her.

"No." Clary answered flatly. "What do you want?"

"Londyn." She said softly. Clary raised an eyebrow.

"What?" The girls green eyes looked into Clary's.

"My name is Londyn." Clary just stared at her. "You haven't asked, so I didn't think you knew."

"Do you need something?" Londyn was quiet. Sighing Clary opened up the door. "I need to get dressed." She walked in quietly and sat down in the chair. Clary took her clothes into the bathroom.

"So you're really my sister?" Londyn asked once she'd come back out. Clary studied her.

"Apparently." She said. Why the fuck was she in her room?

 ** _Four Months later (6 months 2 weeks total bc I suck at math)_**

Clary knocked on Jocelyn's door. She wasn't expecting an answer. Jocelyn had gone out with Londyn and Isabelle. Jace was busy in the library and she had no idea where Alec was. She slipped into the room and shut the door.

The room was much larger than her own. There was a couch and a fireplace along with a desk, dresser, and queen sized bed. Along was wall were paintings. She moved a few to the side, in the hope that maybe there was a safe hidden. No such luck. Clary went through drawers, and cabinets. She didn't expect the Mortal Cup to be hidden in Jocelyn's room. That was too easy. But she did expect to find some clues. She circled the room slowly, thinking. She'd been with these people for six months. She'd learned their habits. She'd learned their schedules and she'd learned what Jocelyn was like. Jocelyn's paintings were beautiful and full of color. Clary'd never gotten her hand on paints. Her father didn't like her drawing as it was. She would've loved to be able to paint like this.

Clary left the room with no new information. She went down to the kitchen as it was noon, and pulled an apple out of the fridge. It appeared that was all she ate. They didn't have much food. The takeout was getting old. Maybe she'd cook them a meal. Alec wouldn't eat it, as he'd think she'd added arsenic to the food, but everyone else would. It had to be better than _Takis._ She took a bite out of her apple and drifted towards the library, where she could hear Jace's music wafting down the hallway. She slipped quietly into the library. Hodge looked up at her from one of the many desks as she made her way towards Jace.

Clary leaned against the railing and waited for the song to end. "That was beautiful." She said. Jace turned to look at her and smiled sheepishly.

"I, uh didn't know you were there." He said. He watched her make her way up the staircase towards him.

"What were you playing?" She asked. They'd grown closer over the last few months. So close, that Clary was actually getting a weird feeling in her stomach. Her father would not approve.

"It doesn't have a name." He answered. "I wrote it." Clary smiled.

"Well, it's very good." She said.

"Don't you have somewhere else to be?" Alec's voice echoed through the room. He stood leaning over the right balcony, watching Clary and Jace's interactions. Jace sighed. Clary craned her neck.

"Don't you?" She snapped back. Alec ground his teeth. Jace stood up, and slipped his hand into Clary's, pulling her down the steps.

"Go train or something, Alec." Jace said, taking Clary out of the room.

"What's his problem?" She muttered. Jace shook his head.

"Alec being Alec." He said letting go of her hand. Clary took another bite of her apple. "Is that all you eat?" He asked.

"Seeing as all you guys have here is junk food, yeah." She answered.

"It's not all bad." He said. Clary shook her head.

"Oh it's bad." She chuckled. Jace was staring at her with a weird look on his face. "What?"

"You don't smile much." He said. "I like your smile. Not as much as mine, but…" Clary looked down and took another bite of her apple. She was uncomfortable. "You want to go out?" He asked cautiously. Clary scrunched up her face.

"I thought you weren't allowed to leave the Institute?" She asked. Jace shrugged.

"I don't like to follow the rules. That's Alec. What he doesn't know won't hurt him." Clary pursed her lips.

"Okay." She said after a moment of thinking it through. Jace straightened.

"Okay." He said. "We've got about two minutes before Alec comes looking for us."

"You want to go now?" She asked. He started walking towards the front of the Institute. Everyone else was gone. It was a better time than ever.

 **I hope you guys liked this chapter**

 **I LOVE REVIEWS AND SUGGESTIONS**

 **Thanks guys,**

 **-Jen**


	8. Chapter 8

**I'm giving up on chapter titles. Can't do it lol**

 **Guys, I struggled so bad with this chapter :(**

 **-Jen**

 **Ch 8**

"I'm going to ignore the fact that you two left the Institute without permission until I finish this." Jocelyn said, taking another bite of the chicken and potatoes Clary had cooked. Alec was sitting at the table with his arms crossed. His food was left untouched.

"Dude if you don't eat that I will." Jace said between mouthfuls. Alec pushed the plate towards him.

"Clary where did you learn to cook like this?" Isabelle asked. "You need to teach me." Jace snorted. Londyn was missing from the table. She was with her father for the night. It was the first time in months.

"You've been inside for six months," Alec started. "And of all the places you could've gone you went to the grocery store?" Clary shrugged. "You two were gone for _hours._ " Clary put a piece of potato in her mouth.

"Aw, did you miss me?" Alec narrowed his eyes. Isabelle snickered. He stood.

"I'll be in the training room." He snapped, leaving the room.

"He thinks you're going to kill us all in our sleep." Isabelle said laughing. "He's pretty adamant, actually."

" _Izzy."_ Jocelyn scolded. Isabelle shrugged.

"It's true." She said. After Isabelle had finished eating, she put her plate in the sink and left the room, leaving Jace and Clary with Jocelyn.

"You two could've asked to leave." She said. "I had to get a call from Alec." Clary rolled her eyes.

"It was my idea Jocelyn." He said. "Every time we go out, Clary is left here with Hodge. She hadn't been out in months. I thought it was an opportunity."

"Nonetheless you could've sent me a text."

"You would've said no." Clary bit back from the sink. Jocelyn looked at her.

"Where did you learn to cook Clary?" Jocelyn asked suddenly, changing the subject. Clary pushed her hair back behind her ears.

"Your cookbooks." She said shrugging. Jocelyn stared at her. "They had your name on them so I assumed they were yours." Sighing Clary put down her sponge. "Idris cookbooks? Father had them in his study. He let me use them." Jocelyn nodded.

"Oh. Those." Clary nodded slowly. Jocelyn seemed to be thinking.

"Jocelyn," Jace said. "Do you know where Valentine is?" Jocelyn shook her head after a minute of silence. Clary was holding her breath.

"No." She said. "Somewhere in Idris." As Clary had told her.

"Shouldn't someone tell the Clave-"

"No." Jocelyn said sharply. She looked at Clary.

"I couldn't tell you where in Idris he is." She said. "All I thought was 'home' and I'd go there. It's in Idris, in woods, but that's all I know."

"Go there?" Jace asked. He didn't know that she could make portals. She didn't plan on telling him.

"Uh, my father has a teleportation ring that my brother and I borrowed." She said quickly.

"That's a thing?" Jocelyn nodded.

"Yes." She said. "He's had that for quite some time." Jocelyn moved around the dining table. "Just please don't do it again without asking me Clary." She said. "Jace."

"Yes Jocelyn." Jace said. Clary rolled her eyes.

 ** _2 weeks later (7 months total)_**

It was Clary's birthday. She didn't expect anyone to remember. She actually hoped that Jocelyn had forgotten. It was too awkward for her. She skipped breakfast to workout on the treadmill. It was today that she realized how much she missed her brother. She was used to waking up early on her birthday, with Jonathan carefully nudging her awake. Together they'd go for a jog around their property then she'd sit at the island and draw while Jonathan cooked up bacon that her father would've gone to get the day before.

Today she wouldn't see her brother. He wouldn't take her for a run. He wouldn't be cooking her bacon. The ritualistic tradition was broken. "Clary." Jace said. She'd been thinking so hard, she hadn't heard him come in. She slowed her running to a walk. "You missed breakfast." She shrugged.

"Wasn't hungry." She answered. Jace cocked his head to the side.

"You okay?" He leaned his arms on the edge of the machine. Sighing, Clary stopped the machine and went to grab a jump rope.

"Why wouldn't I be?" Jace didn't answer. He watched her jump for a good five minutes before she put it away and grabbed her water. "What time is it?" She asked as they left the room.

"Nine." He said. She'd been in the there for three hours. "What are you doing today?" He asked. Clary glanced at him and turned down the hallway towards her room.

"What I do everyday." She said at her door. Jace grabbed her hand, stopping her from going in. She looked down at it. He let go quickly. "Jace?" He shook his head.

"Uh, nothing. Never mind." Quickly, he turned away and headed down the hall to his own room, leaving Clary confused. After he shut his own door, she went into her own, and took a long shower.

It was around noon that she realized she was hungry and would need to make some kind of appearance. She got dressed in respectable clothing, as she'd been wearing a robe since the shower, and went down to the kitchen. Jocelyn was missing but Alec was there.

"I thought Jocelyn said no weapons on the table." Clary said casually, opening the fridge. Alec ignored her, and continued to clean his stele with a rag. Clary pulled out left over pasta and grabbed a fork. "Where is she?" She asked casually, leaning against the counter and taking a bite of the Alfredo.

"Not here." Alec said blatantly.

"Not here as in the room, or not here as in the building?" Alec glanced at her.

"Ask her yourself." Rolling her eyes, she left Alec to his busywork and wandered aimlessly around the Institute. She studied different paintings. Jocelyn painted some of them but most of them were much older. Clary could recognize her mother's because they had same style. It bugged Clary how much alike she and her mother actually were. She wound up back at the kitchen. Alec was gone. She put the empty bowl in the sink. Her head was throbbing. She knew this day was going to awful.

Clary could smell the pot roast from the staircase. She froze at the top. Who was cooking? Dinner was takeout almost every night. Slowly, she descended the stairs to the kitchen and peered inside. Everyone sat at the table, including Lucian, who Clary hadn't seen in months. She avoided the werewolf when he came to the Institute.

"Clary," Jocelyn said from the stove. Clary immediately felt her body tense. No else seemed to pay her much mind. Jace and Alec were digging into the fresh bread while Isabelle gave them looks. Londyn was leaning on her dad. Lucian was reading a mundane newspaper. _Don't you dare say it._ Clary thought. "I made dinner. I uh, know you don't like the normal stuff." She started scooping out some of the stew. "Guys, get it while it's hot." She said. Clary didn't move as everyone else moved to get food. Slowly, Clary made her way over and took one of the last bowls. She sat down the farthest she could from Lucian and ate quietly, but felt Jocelyn's eyes on her the entire time.

After she finished eating she made a quick exit. She didn't want to have a discussion with Jocelyn. She didn't want to _spend her birthday_ with Jocelyn. What she wanted to see her brother, but that wasn't going to happen. She made it up the stairs, very aware that Jace was following her, before he grabbed her arm. "Clary-"

"What Jace?" She snapped.

"Are you okay?" She wasn't crying, was she?

"Yes." She said. "No." He let got of her arm and she backed up. "It's my birthday." She said. Jace raised his eyebrows.

"Why didn't you tell anyone?" Clary shrugged.

"Because its no one's business." She was very, _very_ aware how close Jace was to her. She wasn't uncomfortable. She felt herself calming.

"You amaze me." He said. Clary craned her neck to look up at him. _Why was everyone so freaking tall?_

"How so?"

"I've just never met anyone like you." He said softly. "You're something else." He tucked a loose strand of her hair behind her ear. She found herself leaning into his touch, her hand coming up to rest on his. Clary tilted her head up and met Jace as his head came down. It was as if a spark had ignited. She grabbed the front of his shirt and pulled him closer to her. His hand grabbed the back of her head. "Clar-" He pulled away. Clary blinked.

"Shut up." She breathed pulling him back. He didn't complain. Jace wanted a bedroom, he was thinking it, but Clary kept him right where they were pinned. In the hallway. Where anyone could see them. They were both unaware though, that Alec had come up the steps and seen them, turned around, and went back down.

"I should…" She shook her head, trying to clear her thoughts.

"Yeah," Jace breathed. He stepped away and ran a hand through his hair. They both seemed to be somewhat in shock and Clary found herself, moving quietly towards her bedroom. Without words, they both went into their own rooms and closely closed their doors. Her face was flushed, her eyes dilated. She'd full on kissed him.

At this moment, the mission was compromised. She had feelings for him. The boy in fact, who unknowingly had stolen the attention of her father all those years ago. The boy who her brother hated more than anything else. It couldn't get any worse. Her father was going to kill her. Hell, her brother was going to kill her.

 _Stupid. Stupid. Stupid._ She needed to find the cup and get out because she wasn't sure she could handle being around Jace much longer. Her demon blood seemed to be taking over her emotions. It wasn't like she was angry, as that was how it normally reacted. No. At this moment her body wanted to do things that a fifteen-year-old should not want to do. So, naturally, Clary punched the wall and ended up making a hole.

"What did that wall ever do to you?" Clary had to of jumped five feet in the air. She spun to see her brother standing there, leaning against her bed post.

"Jonathan!" She snapped. "What. The. Hell!" Jonathan smiled.

"Did you think I'd ignore my sisters birthday?" Clary closed her eyes.

"You made a joke. Just a minute ago. You made a joke." She spoke softly. Jonathan blinked.

"I did not." He said. "I simply made a snide remark." Clary wrapped her arms around his body and gave him a quick hug. "I only have a minute before Father realizes I'm gone."

"You have his ring?" He nodded.

"Father was taking a bath. He took it off and left it in his room." He kissed her forehead. "Happy Birthday little sister." Clary smiled. The moment was ruined unfortunately by a knock at the door. "Every time." He mumbled. Clary glared at him. She hadn't locked the door. But whoever was on the other side didn't try and open it.

"Clary?" Jonathan's entire body tensed as he recognized his mother's voice.

 _"Thank you."_ She mouthed. Jonathan nodded, glared at the door and twisted the ring. Sighing she opened the door.

"Yes?" She asked.

"I didn't tell them." Jocelyn said immediately. "I figured it would make you angry." She got that right. "happy Birthday though." Clary didn't smile.

"Thanks." She answered.

"Can I, uh, come in?" Clary stepped back to allow her into the room. Jocelyn moved over to the window and picked up Clary's sketchbook from the chair. Clary tensed but let her go through it. The first drawing was the landscape out her window. She'd worked on it this morning. The next drawing was a sideways portrait of Jonathan. Jocelyn brushed her fingers over it. "Is this Jonathan?" She asked. "He's grown up." Clary didn't want to say anything she'd regret so she didn't speak. "I didn't get you anything. Is there something you want?"

"Something I want?" Valentine wasn't big on gifts. Sure, he'd given her new weapons every great while and occasionally got her clothes. But it was because they were needed. Her old sketchbook back at the cottage was given to her because Valentine had become tired of the bored look Clary had constantly had on her face.

"Doesn't your… father… get you gifts?" She shook her head. "You like art." Jocelyn smiled. "Do you want new pencils, charcoal, another sketchbook?" Clary was quiet. She had no idea what Jocelyn was talking about. Sighing, she put the book down. "Come with me." She moved to the door. "Clary," Sighing, Clary stood up, and followed Jocelyn back to her room. She stopped in the doorway and looked once again at the paintings on the wall.

Jocelyn opened up the bottom drawer of her desk. "Clary." She said again. Clary moved over to her. She pulled out a new pack of primacolor markers and drawing pencils. "I think you'll like these."

 **Guys I'm crying. I could not. For the life of me. Write. This. Chapter. I don't know what it was so hard.**

 **Don't expect a new chapter until Friday. I've got a lot of stuff due this week.**

 **SUGGESTIONS AND REVIEWS MAKE MY DAY!**

 **IT ALSO GIVES ME MOTIVATION!**

 **R &R **

**Thanks guys!  
-Jen**


	9. Chapter 9

**You guys are so funny.**

 **And you're so lucky that my friend bailed on working on a lab with me until later tonight. It gave me some time to finish this chap. (4/13: 3:30pm)**

 **Prepare yourselves. All I'm sayin'**

 **-Jen**

 **9.**

 **C:15**

 **J:17**

 ** _2 Months Later (9 months total)_**

After her birthday, Clary had allowed herself to get closer to Jocelyn. She talked to her. They had conversations. However, they both knew that they would never actually be 'friends.' Clary still hated her guts and would always. "Hey," Jace said, kissing her cheek. She looked up from her book and smiled.

"Hey," She said lazily.

"Alec, Izzy and I are going out tonight." He said, uncomfortably. "We got notification from the Clave of Demonic activity." Clary sighed. She'd been pushing for them to let her go on missions but Jocelyn continued to say no. If something happened to her they'd _have_ to notify the clave and then they'd know she was there. At least, that was the excuse.

"Okay." She said haughtily, moving back to her book. Jace, ignoring her attitude took it out of her hand. "Hey!"

"Pride and Prejudice?" He laughed. "Why do we even have this?" Clary crossed her arms over her chest.

"It was the first thing I found." She snapped. He dropped the book on the library floor and moved quickly onto the couch, kissing her on the lips. Clary relaxed into him and kissed him back.

"Jace, quit snogging and detach your face." Alec said from the door. "We need to get ready." Jace kissed Clary's cheek softly.

"I'll see you later." He said standing. He walked passed his Parabatai and out the door. Alec glared at her as he followed him.

Sighing, she bent down and picked up her book. She gave it a look before throwing it back on the seat next to her. It was a stupid book. Sighing, she lay on her back but realized quickly she was bored and stood up.

She went to the training room for an hour.

She got food from the kitchen.

She finally settled around 11 on sitting on the steps by the front doors, sketching. The group could be out as late as two in the morning. She waited up from them. Well, she waited for Jace. Clary's drawings were nothing extraordinary. A bowl here, a person there. A pen. At one point she drew a dog.

Around 2am, Clary found herself staring at the door. Her pencil absently skimmed over the page. She looked down when she noticed a light emitting from the paper. A rune. She' drawn another rune. Clary ran her hand over the light, and found that the rune was already fading into the paper. It didn't make sense though, as she wasn't using a stele. She pressed her hand on the paper and to her astonishment it disappeared. No, not the paper. Her hand. Clary gasped, dropping the sketchpad on the floor.

Clary stared at the fallen book for a long moment, before bending down and picking it back. She brushed her hand over the paper and went to try and put her hand back in. However, she didn't get far, as the door was thrown open. Jace appeared, blood everywhere. But Clary realized quickly that it wasn't his own.

"Isabelle get Jocelyn!" He ordered, looking up the steps and seeing Clary. "Clary, get Hodge." She found herself staring at Alec, who was in Jace's arms. Isabelle ran passed her. _How could she run in those heels?_ "Clary!" Jace woke her up from her shock. She turned and headed back towards the library.

It was really really late and Clary had only ever seen him in the library. If he had a bedroom Clary didn't know. To be honest, she didn't care that much about Alec. He hated her. She hated him. And the sight of blood got her somewhat excited. If she had it her way, she'd leave Alec to die on his own. But she couldn't do that here. She opened the library doors.

"Hodge!" Clary called. It took a minute, but he emerged on the second floor from the only door.

"Yes?" He asked, yawning.

"Alec's hurt." Hodge came down the spiral staircase wearing a night robe and slippers.

"Infirmary?" Clary nodded and followed behind him towards the room. Hodge pushed open both doors, took one look at Alec and stopped.

"Has someone called a Warlock!" He bellowed through the room. Jace barely glanced at him as he was holding what looked to be a red rag on Alec's stomach area.

"Magnus Bane's on his way." Jocelyn said pushing in passed him, followed by a teary-eyed Isabelle. Clary watched quietly from the sidelines as people ran through the room.

"I-I should contact our parents." Clary heard Isabelle mutter to herself, before leaving.

"People!" Someone clapped a few minutes later. Clary turned to see a _very_ sparkly warlock with cat like eyes. Clary recognized him immediately. Magnus Bane. She'd seen pictures of him before. Valentine had eyes on him as well. "Out of the way!" Jace backed up. He appeared to be in a daze. Clary moved over to him and took his hand. He didn't even register it.

"Jace?" She whispered. He gave her a half glance.

"Clary, take Jace to his room-" Jocelyn started.

"No." Jace said sharply. "I-I need to be here-" Clary pulled him towards the door.

"Jace, there's nothing you can do but let him work." She whispered. She pulled his arm a few times before he slowly left with her. "What happened?" She asked. Jace shook his head.

"We identified five demons inside of Pandemonium. I-it's a night club. We killed all five. Isabelle and I were checking out the rest of the area. Alec had our backs. But we didn't have his. One grabbed him from behind." Jace shook his head.

"Come on." She took him to his bedroom and turned on his shower for him before coming back out. Jace had taken his shirt off and Clary had to take a moment to study his perfectly formed chest.

"Like something you see?" He was trying to make a joke, but it was halfhearted. "I told you I'd be a good model." Shaking her head, she ushered him into the bathroom and promptly shut the door. Tonight was not the night to do _things_ with Jace. She moved his bloody shirt into his hamper and looked around his room. There wasn't a thing out of place. He appeared to be a bit OCD.

"My parents will be here as soon as they can." Isabelle said, moving towards the infirmary. Jocelyn put her hand on her shoulder.

"Izzy, let Magnus work."

"Can I just see him…" She trailed off. Clary moved passed them to pick up the sketchbook she'd left.

"How's Jace?" Jocelyn asked. Clary looked back.

"In the shower as we speak." She said. "Not doing too good." Isabelle closed her eyes.

"He isn't going to die." She muttered. "He isn't going to die." Jocelyn rubbed her back.

"Go sleep." She said. "Or make yourself some tea." Isabelle nodded and moved towards the kitchen. With the sketchbook tucked under her arm, Clary moved back to her room. She sat on her bed and stared at the drawn on piece of paper.

"This is ridiculous." Clary muttered to herself. She sighed, and after a moment of silence tried to put her hand in the paper, and succeeded. Her hand disappeared and as another shock, felt _something._ She wrapped her hand around the object and pulled it. A pen. She'd drawn a pen on the… The pen she'd sketched was no longer on the paper. She slipped her hand back in, put it back and removed her hand. She did this on and off for a few minutes, until her shock wore off. She could hide things in drawings… could Jocelyn do this? Jocelyn had been the one fed angel blood. Clary had just simply inherited some of the angel's abilities. Maybe Jocelyn had acquired skills as well.

Clary was interrupted by a knock on the door. It opened slowly. "Clary?" Jace asked coming into the room. She closed her sketchbook and set it on her nightstand. "Can I…" Clary nodded.

"Come in." She said, though he already had. Jace sat down on the edge of her bed and ran a hand through his wet hair. He now wore a light grey cotton shirt, and sweatpants.

"How's Alec?" Clary glanced at her clock. It was nearing 4.

"Bane's working on him." She said. "Jocelyn isn't letting anyone in. Maybe you should try and sleep." Jace sighed.

"I… can I stay here?" Clary went silent. If Jonathan decided to come… Her brother was slightly unpredictable. He did what he wanted when he wanted. He'd shown up a week ago in the middle of the night shaking and in a sweat. She'd comforted him for the brief time that she could before sending him back.

"Yes." Clary answered.

Clary woke up curled into Jace's chest. His arm was thrown lazily over her. She wondered how long he'd stayed awake, worrying. She slipped out of bed easily and looked at the time. 12. She had never slept so later in her life. Clary pulled out a loose black tshirt and pants. Turning her back, she slipped out of her clothes and put on the new ones.

"Clary?" Jace mumbled. She spun back on him. His eyes were partly open but he appeared to still be asleep. "What's that on your back?" Clary pushed his head back into the pillow lightly.

"Go back to sleep." Didn't have to tell him twice. Jace passed out. She lucked out there.

She brushed her teeth and headed downstairs. The Institute was eerily quiet. She moved to the infirmary and peaked into the room. Alec had his eyes partly open and was whispering to Magnus Bane who had his hand on his. She'd only opened the door a crack, and Alec was too high on drugs to notice the slight creak. Magnus's ears perked though he didn't turn. Who would've thought a Downworlder and a Lightwood... Clary shook her head.  
Knowing that he was alive, Clary went to the kitchen and made some sugary cereal for Jace. She thought it was disgusting, but she wasn't the one eating it. She set the bowl down on her nightstand and nudged Jace.

"Hey," He said sleepily.

"Time to get up." She said. "I got you food." Jace moved to sit up and took the bowl.

"Thanks," He answered, rubbing his eyes.

"Alec's okay." Clary mentioned moving to sit in her chair. "I just checked on him." Jace smiled.

"Good." He said. "That's really good." He ate his sugar and stood. "I'm going to go down. Thanks," Clary nodded.

"Of course." She watched him leave and let out a sigh. Back to her new ability.

It was around dinner time and Clary was just heading downstairs to see what food she could cook up. As she was approaching the end of the hallway, Magnus came around the corner. They both stopped abruptly and stared at each other. "Clarissa." Magnus said carefully.

"Warlock." Clary answered.

"I'm looking for Jocelyn." He said. Why were they even talking?

"She's probably in her room." She wasn't at the moment tracking her mother. Magnus nodded and started walking, only stopping as he passed her.

"You're mad at her." Clary glared at him. "She wanted to take you with her, you know. She had plans to leave when she found out she was pregnant but Valentine escaped the Clave during the Uprising. She never got a chance."

"What's your point Bane?" She snapped. He looked at her sadly.

"You shouldn't believe everything your father tells you." Clary narrowed her eyes. "I helped your mother leave that night. I've been hiding her from Valentine. I know a lot Clarissa Morgenstern. I've been around a long time. I've seen my fare share of liars."

"What is that supposed to mean?" Magnus opened his mouth to respond but was interrupted when Jocelyn came out of her room. Magnus turned towards her. "Does Alec's parents know he's dating a _male warlock."_ Clary whispered before disappearing around the corner. She wasn't blind. She knew what she'd seen in the infirmary.

It was late at night. Everyone was sleeping and Magnus had gone home for the night, claiming he'd be back first thing in the morning. Maryse and Robert were coming tomorrow as well. Clary Slipped out of her room, careful to shut her door quietly, and moved down to the infirmary. She opened the door a crack. Alec was laying in one of the beds, side lamp on with food left untouched on the table. He appeared to be reading a book. He looked over at her as she entered and sighed loudly.

"Go away Clary." He said. She ignored him, and moved over to the edge of the bed. His entire stomach was bandaged and there was a clear Iratze placed on his chest.

"You in any pain?" She asked calmly. Alec eyed her.

"No." He said curtly. Clary sat down on the edge of his head. Alec watched her carefully.

"Damn." She said plainly. They stared at each other, for a minute, like Magnus had done when he'd first encountered her in the hallway. "Do you know what _I_ want Alexander." She asked finally, her voice taking a dangerous turn. "I want you to call off your pet warlock."

"I don't know what the f-" Clary pulled her pocket knife out of her jacket and placed it at Alec's throat in less than a second. He glared venomously at her.

"Please for the love of all things holy finish that sentence." She snapped. Alec stayed silent. "You haven't liked or trusted me since I got here. You've gone running your mouth. Even Magnus Bane, who _of course_ I know about, thinks I'm a flight risk. Is there something in this place, other than my mother, that you're hiding from Valentine? Because honestly, my mother isn't that much of an important person. I'm not that much of an important person." Alec's eyes sharpened. "Here's what you're going to do. You're going to call off your boyfriend."

"He is not-!"

"Really? She whispered. "Really you're going to pretend _that_ isn't happening. You're face is an open book. At least, to me it is. You're gay- ah ah ah." She pushed the knife deeper into his neck drawing a bit of blood as Alec tried to make a grab at her. He was too slow. He did have some pain and it would hurt a lot more in a few hours. "Alexander Lightwood is gay and he's dating a warlock. Of all warlocks, Magnus Bane!" Alec was beyond angry. Clary was having fun though. She let her demon side take over a bit. She wouldn't try and purposely hurt him, but she needed him off of her back. "How long ago did that start. 1 week? 2 weeks? 3- oh there it is." She was very good at reading people and he blinked at 3. You've been dating him for three weeks. That's something. Now listen. You are going to call off your _pet._ You're going stop being a complete and _utter_ asshole. Because the next time I get shit, _I'm going to cut you open like a piñata._ " Alec snorted.

"You don't scare me Clary." He said. Keeping the knife at his throat, she leaned in.

"I think I do." She whispered in his ear. She pushed his head back into the mattress hard and stood up. "Good night Alec. I look forward to seeing your parents tomorrow." Alec tensed.

"Clary." He said, his voice cracking. She turned back at the door. "You… you wont…" She smiled then, and left the room. She wasn't going to tell his parents. But it was fun to see him squirm.

 **Guys, I love evil Clary. She's just so entertaining.**

 **This chapter is full of STUFF!**

 **I hope you liked it**

 **PLEASE GIVE ME SUGGESTIONS FOR FUTURE CHAPTERS! I TAKE EVERYTHING YOU SAY INTO SERIOUS CONSIDERATION!**

 **I will also consider doing flashbacks. BUT ITS ALL UP TO YOU GUYS. And I need to know what you guys want them to be for.**

 **Ask me questions I answer back :)**

 **R &R I love you guys**

 **-Jenna**


	10. Chapter 10

**As an apology for not updating ALL FREAKING SUMMER I have included a bit more (detailed) Malec AND Clace.**

 **Also this limited POV is starting to drive me insane haha**

 **-Jen**

 **10.**

 ** _One week Later_**

"I think I know where the cup is." Clary said abruptly a week later. Jonathan blinked. He was there under Valentine's orders. To make sure everything was going to plan. He'd been expecting her to bring up Alex's accident but really nothing else.

"That was fast." He said leaning against the wall of her room. Clary, in her excitement took Jonathans hands in hers.

"It's in a painting." Jonathan blinked. She had to be joking. His hands tightened in hers, his face tight.

"A… painting…" He said slowly. Clary understood his hesitancy. She hadn't yet explained her new found ability. She released his hands and picked up her Sketchbook and pen.

"Watch Jon." She slipped the pen into the paper and showed him the sketch. She then pulled it out. He showed no expression.

"How did you do that?" He asked.

"A rune." She threw the pad back on her bed and took his hands again. "I think Jocelyn can do this too. It would make sense."

"That's a pretty good hiding trick." He responded, holding her hands tighter. He liked this kind of attention from her. It didn't feel forced, like recent meetings had been.

"I've been playing with it on and off. I discovered it last week." Jonathan smiled then.

"You and your gifts little sister." His said quietly putting a hand on her cheek. "You never cease to amaze me." He kissed her cheek. Clary smiled.

"I got a little pissy with Alec last week." She muttered.

"really?" Jonathan kept the smile off his face.

"Yeah." She said. "I might've pulled a knife on him while he was in the infirmary." Jonathan snorted.

"Good for you Clary." She shook her head unamazed by his ignorance.

"Not really Jon. It could've caused problems." Jonathan laughed.

"What kind of problems?"

"For one he's dating the warlock." Jonathan raised his eyebrows and moved to sit on the bed. Clary followed him.

"Alec Lightwood is gay?" Clary nodded. She let her legs dangle on the bed and laid on her back. "Hmm." They sat there in quiet for a few minutes, thinking over the information gathered. "I've missed you Clary." He finally said. "More than you know." She sighed.

"Yeah, I want to go home."

Jonathan paced back and forth in front of Valentine's study. He'd been in there all evening and Jonathan was growing impatient. Taking a deep breath he knocked again on the door and waited. "I'm busy Jonathan." Valentine's voice came through loud and clear from the other side of the door.

"I have news concerning Clary." He said quickly. "It's-" The door opened and Valentine's angered face appeared. Jonathan stood his ground.

"It can't wait?" He bit back. Jonathan could hear voices on the other side of the door talking.

"Not when it concerns the cup." The voices died down instantly. Valentine paid them no mind. His face changed considerably and he stepped back to let his son into the room. Jonathan looked around for the source of the whispers but found no one. He turned back at his father in confusion. He didn't explain.

"Speak then." He said placing himself back at his desk. Jonathan approached.

"Would giving mother angel blood give her powers?" He started. Valentine blinked.

"Possibly, though I never really considered it." He said honestly. "What of it?" Jonathan explained what his sister had told, and showed, him. At end of the brief explanation Valentine was silent. He leaned back in his chair and put his hand to his chin.

"She's sure it's in the Institute." Jonathan said finally. Valentine's eyes darted to his.

"If this is in fact something your mother can do, it could be anywhere Jonathan." He shook his head.

"Wouldn't she want to keep it somewhere she could always see it? She would never think that you would think she could do something of this magnitude. Or she could've kept it with someone she trusted with her life." Valentine shook his head.

"Your mother did love painting." He muttered. "I always thought she'd be able to sell a few of them. No doubt she could've given them to the warlock. He'd be able to hide its power from my detection." Jonathan paced shaking his head.

"Maybe… we should scare her into moving it." He said slowly. Valentine worked his jaw.

"You think I trust you enough to send you out?" He said. "After what you did last week?" Jonathan got a glint in his eye.

"Though I would enjoy wrecking Bane's home, I understand why you are angry." He said calmly. Valentine rolled his eyes.

"Don't suck up to me Jonathan." He snapped. "You nearly killed the boy." Jonathan smiled.

" _I_ didn't do anything. I merely ordered someone else to do it. And besides," He added before Valentine could interrupt. "He was getting in Clary's way." Valentine growled.

"Jonathan. You. Were. There." He shrugged. "Jonathan-"

"I'll be training if you need me father." He said turning his back on Valentine. As left the room, he could've sworn he heard the voices begin to whisper again.

Magnus trailed a line of kisses down Alec's neck, eliciting a slight groan from him. "Magnus…" He muttered, his hand caressing Bane's upper arm. Magnus moved lower, to Alec's bandage before stopping.

"This should've healed by now." He muttered. Alec looked down at him.

"Way to be a buzz kill." He whispered plopping himself further into his pillows. Magnus kissed his bandage free muscled chest. His cat eyes gleamed.

"I'm sorry." He whispered, coming back up to peck Alec on the lips. "I'm sorry." Alec sighed.

"At least it doesn't hurt." Alec said. "Not that… that would bother me much." Magnus chuckled.

"You're so cute." He said running his hands through Alec's hair and brushing his lips against Alec's earlobe. He chuckled, turning in Magnus's arms and putting one knee between his legs.

"What are you and Jocelyn up to?" He asked, catching Magnus off guard. He traced a finger down his chest. "You've been holed up in her office all week."

"Maybe I'd tell you if you'd tell me what the scar on your neck is from." Magnus said back taking Alec's hand in his.

"It's nothing." He answered, moving in to kiss Magnus. He moved his head back.

"You started this." Magnus said softly. Alec pursed his lips. "Your neck looked perfectly fine when I left and when I came back you had that nasty thing. It's not like you had anything to hurt yourself with. You couldn't even get up." Alec shrugged.

"It's not that big of a deal." He answered.

"Did someone hurt you?"

"Magnus." Alec pushed himself into a sitting position Magnus remained sprawled on the bed, his hand supporting his head. They stared at each other for a long moment.

"Clarissa poses a threat." Magnus sighed, relenting in the conversation. "If Valentine's looking for her, he probably found her when she left. That's what I've been talking to Jocelyn about. I've been trying to get her to move." Alec was taken aback.

"Do you really believe she ran away from Valentine?" He asked after a while. Magnus had his hand on Alec's leg.

"No." He answered. Alec closed his eyes. He wasn't the only one that didn't trust her. Hell he knew she had a dark side. When Alec's eyes reopened Magnus was staring at him. "It wasn't her that did that to you. Was it?" Alec didn't agree or disagree, giving Magnus the answer he was looking for. "Alec-"

"I've been giving her a hard time and she told me to back off." He said neatly.

"She _hurt_ you."

"Just leave it alone." Magnus jumped into a sitting position.

"You're mine Alec. She hurts you, she hurts me. I'm going to deal with this." Alec grabbed Magnus's arm.

"Just-don't. please."

"Why? Tell me why before I turn her into a pumpkin the color of her hair." Alec chewed the inside of his cheek.

"She knows." He muttered. "That. We're… That I'm…" Alec shook his head. "Just please don't do anything. I want her to think she's won." Magnus just stared at him, a frown on his face.

 ** _Three Weeks Later_**

"Clary, just… talk to me." Jace said following her into her room. She'd decided after her meeting with her brother that her time would be ending their soon. Jonathan had started showing up more frequently and the chance that he appeared while she was with Jace made it all that more dangerous. On top of that, if he knew that she was with the _other Jonathan_ she was afraid she'd see the very worst of her brother. A side that he kept hidden from her. Jonathan despised Jace more than anything in the world.

"Jace, not right now." He closed her bedroom door and crossed his arms over her chest.

"What have I done to you to make you so upset with me?" He asked. "I can never get you alone anymore. Are you jealous of my gorgeous features? Is that it?" Clary rolled her eyes. He was trying to make light of the situation. In fact, there was no situation because there was no Jace and Clary.

"We... You… I…" Clary sighed. "There is no US, Jace. We won't work out. It's nothing you did. I just… need space." Jace shook his head.

"I have been giving you space Clary. For three weeks, I have left you alone. I need _some_ explanation."

"Why are you so clingy?" Clary snapped turning on him. She was trying to keep her demon at bay. She understood why he was upset. She was very upset too, but this confrontation was upsetting her even more and her demon was pushing at the edge. It had been pushing more, recently. Another reason why she needed to leave Jace alone. The demon didn't want to hurt him. It wanted what Jonathan's demon wanted. Clary took a deep breath. "Jace…" Without warning he walked up to her, clasped his hands on both of her cheeks and kissed her. And she just wanted to melt. She leaned into his body as his hand supported the back of her bed, keeping her to him. When he pulled away, Clary was left speechless, unable to come up with an excuse.

"You can't tell me you didn't feel anything." He said.

"I…" She considered lying. She really did. Sighing she walked up to him, grabbed him by the collar of his shirt and pulled his head down to her height. So much for avoiding distractions and the anger of her brother. What the hell.

"Father wants you to proceed." Jonathan said the next time they met. Clary shook her head.

"It might not even be in the Institute." She said. "And Jocelyn is always here." Jonathan shrugged.

"The longer you're here Clary, the better chance she'll move it. It's probably somewhere she can always see it. You're the one who said you wanted to come home." Clary nodded slowly. Jonathan pulled her into his arms. "Well then little sister, its time to finish this." Clary rested her head on his chest.

"What am I supposed to do if I find it Jon?" She asked. "Father wants Jocelyn. He told me that." Jon kissed the top of her head.

"Hang one of your sketches on the window." He said. "I can see it from the ally. We'll come." Clary sighed. "I'll be watching little sister."

 **I'm trying to push this along. I wanted this to be a quick story. Not a long one like all my others.**

 **Thanks for reading**

 **R &R PLEASE!**

 **-Jen**


	11. Chapter 11

**Ch. 11**

 ** _Three Days Later_**

As Clary woke up early, she knew something felt different, wrong. She knew she was stressed. She could feel it in her muscles. She flexed them, trying rid herself of the soreness. However, that did nothing. As she got dressed to go to the gym she felt it. The muscle pain turned into stomach pain that made her entire body feel like fire. The pain that she'd had as a child was happening to her again. She'd grown used to the dull thud of her demon trying to get it's way past the angel. The severe pain she'd used to have from it, had disappeared almost completely. She knew it shouldn't have happened again. At least, if her father's theory had been correct. If not, what was the point of all those stupid tests?

Clary found her way back into bed, shedding her clean clothes in the process. This time was different. She didn't have her brother's comfort to help her through it. She wasn't used to this kind of pain anymore. She closed her eyes and gripped the pillow.

"Clary?" Someone knocked on her door. She peeled her eyes open but didn't respond as Jace peered into the room. "Are you okay?" He asked softly, entering cautiously.

"Can you just… go away?" She asked, her hands tightening on the sheets. Jace shut the door softly and moved over to the bed.

"Are you sick? I thought I'd see you in the gym this morning." Clary didn't say anything. She took a deep breath. Slowing down her heartbeat did seem to help. Jace sat down on the edge of her bed. "Do you need me to get Magnus-"

"No." She said abruptly. "What time is it?" Jace sighed.

"Around Noon. Are you sure you don't want me to get someone? You look really-"

"Jace." Clary snapped. "I'm fine." She hoped. It had been so long since she'd felt like this. He put a hand on her back.

"Do you need anything?" He said, his voice softer than before. The comfort, him rubbing her back, was what she needed. What she _really_ needed was her brother. He was her crutch, just as she was his. Jace, this Jonathan, was not her brother. Him being here when she was at her weakest was like another betrayal. She didn't answer him. "I'll get you some water." He said finally, leaving Clary to go to the kitchen. She pulled the covers over her head, and tried to sleep. She could imagine her brother holding her. Asking her _1-10?_ She would've responded _9._ It had been a _long_ time since she'd felt _this_ much pain. It needed to go away. She had a job to do.

"Jace, where's Clary?" Jocelyn asked. She was cooking up what looked like spaghetti. Magnus was leaning against the counters, both hands clasped firmly on the granite. Jace walked around him to get the glasses.

"In bed." He answered simply. Jocelyn turned away from her cooking. Realizing she was staring at him he added. "She's sick. Shaking. Sweating. Looks like she may have a fever." Magnus scrunched up his face. Jocelyn blinked. "What?" He asked. Jocelyn shook her head and turned back to the food. Sighing, Jace filled the cup.

"Magnus maybe you should look at her-"Jocelyn began.

"She said she doesn't want him to." Magnus waved his hand in the air.

"Besides," He responded. "My services are not free." Jocelyn narrowed her eyes. "But I'm curious as to why not? Am I not pleasant to be around?" Jace snorted.

"Your fees aren't." He responded lightly, heading back towards Clary's room. He could sense their eyes on his back as he walked past them and out of their line of sight. Clary was not in her bed when got back. He set the water on the nightstand and knocked on the bathroom door.

"Clary?" He asked. He could hear her gagging. "Are you okay?"

She bolted for the lock before turning back to the toilet again. She heaved nothing into the bowl. Things were hazy. Everything in her body screamed. Slowly, the need to throw up passed. On wobbly legs she stood. She looked at herself in the mirror and blankly wiped away some of the black blood on her bottom lip. _Black._

"Clary?" Jace asked again, knocking. She jumped.

"Yeah." She said softly, her voice cracking. " Yes, I'm fine." Her eyes were their normal color. No problem there. Shaking her head she looked around the room in a panic. What normally helped her with this? A bath? She didn't really want a bath. Not at all.

"Please open the door." Clary closed her eyes. She kept reminding herself that he cared about her. With shaking hands she opened the door and came face to face with Jace. "You look pale." He said. "Are you sure you don't want me to get Magnus?" She didn't answer him.

"I just need sleep." She answered as she slowly made her way back to the bed. Jace followed carefully at a slight distance. Clary realized then that she was dressed in only her undergarments. "Can you grab my sweats?" She asked with a sigh, plopping down on the mattress. "bottom drawer." Jace quickly retrieved the pants as well as a tshirt that was lying on the floor.

"Let me…" Jace helped her into the clothes. Then under the covers. "Take a sip of water." He said handing her the glass. She did as she was told, though the swallow seemed forced. He set the glass back down and turned to leave the room, flipping off the light switch.

"Jace?" Clary whispered.

"Yes Clary?" Her emerald eyes peered at her from between the fabrics.

"Will you stay with me?" Damn the consequences. At that moment, she'd decided to think for herself. Not her brother.

"Of course."

Jonathan did his normal routine for the morning. He got dressed, trained, had a small breakfast, then portaled to the other side of the world where it was night and he would wait for Clary's signal. That, or any sign that she was in danger. Although he was a ways off from her window, or even the institute itself, he could see pretty clearly through her window. He normally would watch her draw, herself propped in the chair scribbling aimlessly while glancing outside. He hoped she was looking for him. He also knew that she would never see him, because he was very good at staying hidden. Today was different. Today, he woke with a bad feeling in his chest. There was little to no movement in her window. Most of the lights were off. Jonathan decided after careful deliberation to get closer. He needed to know that his little sister was okay. He moved to a point off the institute grounds, where he could see fully into her bedroom. A small lamp was lit on the nightstand and what he saw beyond that had him shaking to the core.

Clary was laying under the covers of her bed and with her was Jace-the _other_ Jonathan. He was in bed with her playing with curls of her hair. That was _his_ job. Jonathan had half a mind to portal into the Institute where he would tear the boy to smithereens. However, he knew that it was not possible with Valentine's care for the boy. Jonathan's plans for the future didn't include his monster of a father. When he was gone, or no longer a threat, Jonathan would make _sure_ the other Jonathan suffered. For the remainder of the time he spent there, as instructed by Valentine he imagined slowly destroying him in the confines of the basement. Not once did he wonder why his little sister was in bed so early.

Clary woke up the next morning hungry. The pains were gone. Her muscles no longer hurt. She stretched before standing on wobbly legs and leaving a sleeping Jace to go to the kitchen. She walked into the dark room, and flipped the light switch, turning on the lights. Digging through the fridge, she pulled out an apple from the bag and ate the thing to its core. Still hungry she dug in the cabinets until she found crackers. She ate half the box without hesitation.

"Clary?" Isabelle asked walking into the room. Clary smiled at her, ignoring the fact that her face was full of food. "I heard you were sick." Clary shrugged.

"Yeah, a 24 hour thing. I'm okay now though." Isabelle looked at her questionably. It wasn't normal for Shadowhunters to get sick. If there was an illness it was usually life threatening.

"I came in to check on you around six, but you were already in bed." She said, walking over to the pantry and pulling out the frosted flakes. Clary didn't say anything. She just munched on her crackers. "How're things with Jace?"

"Fine." Clary answered, putting what was left of the crackers away. She made herself a cup of coffee.

"You should be careful with him." Isabelle added. "He's been through a lot and he's like a brother to me."

"I'll take that into consideration." She said, heading back upstairs. Clary had been living there for more than eight months. Not even a year. It had been random for Isabelle to bring up the protection of Jace. What about her? Living with Valentine, Clary had gotten everything. At least she felt like she had. Jace had too. But in everyone else's eyes, and from Clary's fake testimony, Valentine had been a monster to her. From Isabelle's words, Clary assumed they all knew that he'd been the one to raise Jace. But did Jace know? Had he been told that truth?

"Hey," Jace said groggily as Clary walked into the room. "You look much better." Clary smiled weakly as she sat down by his waist at the bed.

"Much." She answered. "Thanks for staying with me."

"No reason to thank me." He said. They were silent for a few minutes, both taking in each other's presence. At some point during the night Jace had removed his shirt and slipped under the covers.

"You don't talk about him." Clary said before she changed her mind. Jace placed one arm behind his head on the pillow.

"Who?" Jace asked. Clary shrugged.

"Your dad." Furrowing his brow, Jace got into a sitting position.

"My father?" He blinked.

"Just something Isabelle said downstairs… about you having a hard life." Jace sighed, and rolled his eyes.

"Isabelle." He muttered. "It's been years… I saw him get killed." He paused. "When I was young. Murdered in our house."

"Oh." Clary was surprised. That's how Valentine had gotten rid of him? That was… awful to say the least. "I'm sorry." Jace shrugged.

"Like I said it was years ago. Isabelle always feels the need to protect me. I'm over it though." Clary didn't believe that. If Valentine had died in front of Clary, she would've been traumatized for years. "He wasn't around a lot growing up. I was on my own most of the time… But he always made it home for my birthday." Jace smiled. "Always." Shaking his head, he studied Clary. She set the coffee on her nightstand as Jace pulled her into his arms and rolled her onto the opposite side of the bed. He kissed her softly on the lips. "You aren't contagious are you?" He chuckled. In response Clary kissed him back with more force, pushing him into the mattress. His hands rested on the waistline of her sweatpants, slowly slipping their way under her shirt and up the bare of her back as they kissed. He nipped the crook of her neck, sending chills down her spine. "Thank you Clary." He whispered in her ear.

 **Kind of just a filler chapter. Hope you enjoyed it.**

 **Please R &R**

 **-Jen**


	12. Chapter 12

**I dislike school. And politics. I have been sick for an entire week twice in the last three weeks and I am so done with it. And of course, class work.**

 **You guys are awesome. Honestly. Truly.**

 **-Jen**

 **Ch.12**

"What have you done?" Valentine's cool, collected voice cut through the silence of Jonathan's room. The door was open but the room was dark, with only light from the moon, shining through the window. From what Valentine could see, the place was trashed. He'd been gone most of the evening, unaware of the havoc Jonathan had been wreaking.

Valentine did not enter the room, as he could not see Jonathan and he knew that he was there lurking in the shadow. He crossed his arms across his chest and waited. "Clary needs to come home." He said from somewhere in the left quadrant.

"Jonathan." Valentine sighed. "She will. Once she gets me the cup." Jonathan stepped into the moonlight. His arms were crossed as if he was holding himself.

"She's getting distracted." He answered. Valentine waited for his son to explain but he did not. He just stood there staring out the window.

"Trust your sister." Valentine said.

"I do."

"Then what's the problem?" Jonathan turned. The look on his face would scare anyone. His jaw was set, his hair a mess. He didn't want to say it. Shouldn't have to say it.

"Him." Was all Jonathan said, turning and kicking his broken bed. Valentine sighed.

"Do you know how expensive this furniture is Jonathan? Do you expect me to replace it all? It was old, _expensive, handmade furniture!"_ He didn't answer. "For angels sake!" Jonathan ground his teeth.

"He and Clary are in a relationship." He said blankly. For once, Valentine didn't have a response. He stared at Jonathan and he stared back. The house was once again, silent. "I'll sleep in Clary's room." Jonathan muttered, picking up his steele and Seraph Blade and pushing his way past his father.

"Are you sure?" Valentine said as Jonathan reached her door. He stopped and glanced back.

"They were in bed together." He said. "I know what I saw."

"Bed." Valentine said. "or _bed."_ Jonathan suppressed a growl.

"Bed." He answered. "She was sleeping. He was playing with her hair." Valentine was silent. "I need to kill something." Jonathan muttered under his breath too quiet for Valentine to hear, before slipping in Clary's empty bedroom.

 ** _Two Days Later_**

It was early on a Saturday morning. Alec, Isabelle and Jace were gone. To where, Clary had no idea. She'd been walking around the institute aimlessly when she neared Jocelyn's office. Immediately she picked up the angst in Jocelyn's voice as she spoke to Magnus. "I don't think it's wise." Jocelyn said. Clary stopped a good fifty feet back, worried that Magnus would pick up on her eavesdropping. At least if she was back there and he sensed her, she could claim she couldn't hear anything. A normal shadowhunter's ears wouldn't have been able to pick up the conversation.

"Jocelyn, do you understand the situation?" Magnus asked. "I haven't sensed _one_ of Valentine's scouts in about seven months. There could be a chance he's found you. You need to leave." Clary tensed.

"Maybe he gave up on New York." She said halfheartedly. Sighing she added "My family is here. My life is here. I can't just-"

"You've done it before." Silence stretched in the small room. Finally Jocelyn sighed.

"I can't do it again. I _won't_ do it again."

"Do you know what could happen, what will happen, if Valentine gets ahold of you? Do you know what he'll do to the world?" Jocelyn was silent. "Jocelyn, if he gets the-"

"I know Magnus." Jocelyn snapped. "I know." Magnus sighed. Silence stretched on. "I'm going to take Londyn over to Luke's tonight. If you're so sure there aren't any of his men out there."

"You know what Jocelyn? Do what you want. Don't listen to an old, senile Warlock. Go get caught by the Circle. Have fun." Magnus opened the door to the study and walked down the opposite direction of Clary, disappearing around the corner. Turning, Clary went in the opposite direction before Jocelyn could see her and slipped securely into her own room. She locked the door as she thought through the information given. Had Magnus really not sensed her? Had she really heard all that? Taking a deep breath, Clary curled up in her chair with her sketch book and drew. She drew her brother. She drew her father. She even drew a picture of Jace. After what felt like hours, she stretched her bored muscles and looked up towards the door, Only to gasp.

"What the _fuck_ Jonathan!" She hissed, standing up. He stood off the side by her dresser, watching her silently. He didn't smile or greet her warmly. He seemed cold. Off. "What are you doing here?" She asked after her heart settled. It was barely midday.

"Couldn't sleep." He answered.

"How did you get Father's ring?" Clary stood up and made her way over to him. When she went to touch his arm, he moved away from her, as if she'd shocked him.

"He gave it to me." It was the truth. Jonathan had let his anger build up, choosing to tear the house apart as a way to calm. Valentine had finally relented and given him the ring.

"Its not safe for you to be here." Clary said. "If the others come back-"

"Your _friends_ are gone for the day." He said. "The Pandemonium, if my sources are correct."

"Magnus Bane is here. So is Jocelyn and Londyn-"

"So the thing has a name?" Clary frowned, choosing to try and approach her brother once again.

"Jon, what wrong?" She asked softly. "Why are you here?" She took his hand, even as he tried to pull away. She could see, _smell_ the wet blood on the hem of his white shirt. When could she smell blood? Jonathan pulled her hand up to his lips, and kissed her knuckles. He kept her hand there, as he took in her scent. Clary didn't say anything, only watched as her brother struggled.

"I love you Clary." He said finally. Love. A word Jonathan had never expressed before. Her eyes widened at sound on his lips, and she pulled him into a hug after the shock had worn off. "You won't leave me." He said into her hair. "Promise me you won't." Clary closed her eyes. Her brother sounded so broken. She wondered if something had happened at home.

"I won't Jon." She answered. She loved her brother but he was a prison. Her prison. And she'd been sentenced for life. After her brother seemed to of calmed down Clary told him what she'd overheard.

"I think the cup is in there." Clary said, referring to the office.

"You think?" Jonathan asked, dubiously.

"I've never been inside. The door is locked and there's a kind of humming coming from it."

"Like a spell." Clary nodded. Jonathan worked his jaw, thinking. "It's most likely a warning." He said.

"What should I do?" She asked him. Jonathan smiled for the first time since she'd noticed him watching her.

"You should wait. I'm going to tell Father." Clary sighed.

"Okay." Jonathan kissed Clary on the forehead.

"Nice drawing of Jonathan." He added, surprising Clary once again as he disappeared. Later that night, after she'd had dinner, she noticed the sketchbook had been moved. And Jace's picture had been ripped out.

 ** _Four Days Later_**

 _"Clary,"_ Clarissa blinked awake. Groggily she turned to look at the clock on her nightstand. It was only 3am. Sighing, she turned back onto her side, hugging the comforter close to her chest. Closing her eyes, she tried to find sleep. _"Clarissa."_ There. She'd heard the voice. It seemed to be coming from everywhere but nowhere. Slipping out of the covers she peered around the room. Slowly she opened the bedroom door and peered out. _"Clarissa."_ She felt almost like a tug in her chest. She followed the voice down corridors and steps into what appeared to be the basement. A creepy basement made of stone blocks and filled with cobwebs. It was at a dead end that she stumbled upon the mirror. _"Come closer darling."_ Clary could make out the faint outline of a woman. She had long black hair, and a slim body. However, her eyes were not there. Snakes replaced them.

"Who are you?" Clary asked in awe. She was not frightened strangely. The woman seemed oddly familiar.

" _I am many things."_ The woman answered. " _But you may call me Lilith."_ Clary blinked. Where had she heard that name before. " _You are in search for the Mortal Cup."_ She added when Clary said nothing. " _And Valentine is coming._ " Clary eyed the woman credulously. " _Am I wrong?"_ She asked, with a click.

"N-No." She answered.

" _I can help you find it, or get through the Warlocks spell undetected at least."_ Clary took a step back.

"I've been here for months. Why are you just now talking to me?" Lilith seemed to get larger in the mirror as if she was getting closer.

" _Your mind was not yet open to me."_ Clary blinked.

"This… isn't real." She said. Lilith nodded.

" _I am using your dreams to connect with you, you are right. I cannot leave my dimension."_ Clary felt a bit safer knowing this wasn't real. She let out a breath she didn't know she was holding. _"Do you know what is wrong with you child? Why you are sick?"_ Clary shook her head. " _It is my blood inside you. You and your brother."_ She started pacing within the mirror. _"However Valentine also gave you Angel blood."_

 _"_ It's fighting. I know." Clary cut in. Lilith nodded.

" _Correct. And it will settle. It all depends on you."_

"Me?"

" _Yes. Your personality. How you act. You will always be strong. You will always have a heart that your brother does not. But only one can truly win._

" _As for the cup, it is something hidden. What you see is not what is there."_


	13. Chapter 13

**The Shadowhunters TV show is getting better. Slowly. They fixed the graphics! Yay! Next is the god awful acting which in part I think is because of the script. That will be fixed too. New Scriptwriters wrote all the episodes after ep 3 so if you didn't like Shadowhunters in season 1 (I didn't but I watched and cringed anyway) I recommend giving it another shot. They are slowly getting better. ALSO, there are rumors that Sebastian HAS been casted and will be in the second half of season 2. No one really has confirmed this because they can't confuse the people who haven't read the books.**

 **On to the next chapter!**

 **R &R**

 **-Jen**

 **Ch. 13**

"Jace we really can't be doing this." Clary said between kisses. They sat on a couch in the back of the library. Clary _had_ been reading a book peacefully before Jace had found her. From there, the book found its way to the floor and Clary underneath Jace as the sun shown down from the Mosaic window. In response to Clary's protests Jace moved to her neck, gently nipping her skin and sending shockwaves through her body. Clary sighed "Ja-"

"Jace." Alec's steel voice cut through the quiet of the room. Jace sat up, leaving Clary's legs behind his back. Alec's face looked strained as he fought back a glare. "We're heading to Hotel Dumort."

"Vampires?" Jace asked standing and cracking his neck. "What they do this time?" Alec shook his head in annoyance.

"The Clave suspects they've kidnapped a few mundanes that have gone missing in the last few days."

"Wouldn't that break the Accords?" Clary asked swinging her legs to the floor. Alec glanced at her.

"If they hurt them then yeah." Jace answered.

"Sounds serious. I thought you guys only did recon."

" _Usually_ do recon." Alec said. "Sometimes we get to fight." Clary laughed.

"Once since I got here." Alec narrowed his eyes.

"And how would you know?" Clary stuck out her tongue. Jace snorted.

"Okay guys real funny. Where's Isabelle?" Clary followed close behind them as they made their way out of the Library.

"Getting ready." As they made their way to the training room the group passed Jocelyn as she came out of her office. As the door closed Clary got a glimpse of a leather couch.

"Oh boys I'm glad I caught you." Jocelyn said. She looked troubled as her face was red and somewhat sweaty. "Take Clary with you." Clary watched as every muscle in Alec's body clenched up. She smiled.

"Really?" She asked giddily.

" _Really?"_ Alec bit out. Jocelyn's eyes snapped to Alec.

"Alexander are you aware of how many vampires live in that hotel? That is their sanctuary. Their home. And there are only three of you. Unfortunately this is a growing situation and it needs to be handled quickly. The Clave believes you are capable but I think it would be a good idea to have backup."

"Then why don't _you_ come?" Alec sounded like a baby. Jace shot him a glare.

"I am running this Institute. That is why. You're taking Clary because she is a good fighter. Maybe even better than _you_ Alec." He bit back a retort. "Besides I've already told Isabelle. She's grabbing clothes for you Clary." Jocelyn continued down the long hallway and for a moment Clary liked the woman. Alec turned on her.

"If you do _anything_ to mess this up-"

"Come on Alec, it'll be fine." Jace said. He was always protecting Clary and although she knew it was out of his affection for her, she didn't like it. No one needed to defend her.

Twenty minutes later and there were on their way to uptown Manhattan. Clary was dressed in dark leather and she was comfortable in it. Isabelle hadn't gone too crazy with the wardrobe.

The Hotel Dumort was beautiful on the outside. At one point it must've been a popular hotel. Clary took in her surroundings. As she hadn't really gotten to adventure in New York this was all new to her. Alec was giving everyone instructions but she didn't really focus until he was in her face.

"You. Stay here." Clary put her hands on her hips.

"Excuse me?" The arrogance was in his voice as he spoke to her. It took all of her willpower not to punch him in his face.

"If anyone runs out you'll be here." Clary laughed and looked up at the sky.

"It's noon! No Vampire is going to run out here!" It was the most ridiculous excuse she'd ever heard. Sure, she'd never really _fought_ anyone to _kill_ them but it wouldn't be too hard. She'd trained excessively since diapers.

"True." Isabelle muttered looking away.

"Just stay here." Alec snapped.

"You mean stay out of your way!" Their voices were growing louder by the second and it could easily alert the vampires.

"Guys can we not fight?" Jace said once again becoming the referee. "Clary, just… stay out here. If we aren't back in thirty minutes we probably need you."

"Won't." Alec muttered.

"Might." Jace said, pressing a kiss to Clary's cheek. She crossed her arms over her chest but didn't argue. Instead she plopped herself on a bench across the street by a park as she watched them disappear behind the construction fence.

A few kids giggled as they played on the swing set and mundanes walked by with their dogs on leashes. Some were jogging. This was just a normal day for them. They went on with their lives, unaware of the magic and mystery that enveloped their world.

Thirty minutes went by and no one came out. She gave them fifteen more minutes, just for the benefit of the doubt. However by then she was so worried her heart was thrumming in her chest. She stood up from her spot on the bench and slowly made her way into the gated front of the building. She could see immediately where the group had gained access. It was obvious and right out front, probably not the best idea. Clary silently yelled at them before making her way to the back of the building where the ground rose to the second floor. She pulled at the doors carefully, afraid of making a noise. They were locked.

Sighing she took the knob of a steel door with both hands and yanked. With a loud creak, the door flew open. The room beyond was dark and she had to strain her eyes to make out a narrow hallway. With her Seraph blade extended and ready she stepped into a dank smelling space.

As soon as the door shut behind her, her senses opened up. Her eyesight adjusted so that she could see near perfect and her hearing improved drastically. In fact she could hear voices from what sounded like upstairs. She came to a kitchen area that hadn't been cleaned in ages. Grimacing she peered through the double swinging doors into what was once a fancy dining room. The red wall paper was ripped from the walls and the floors were coated in a thick layer of dust. "Come on Clary." She whispered to herself before slipping into the room and dashing across to a heavier set of doors. She could hear moving beyond the door. There was a shuffling of feet and Clary expanded her hearing.

"Raphael will have our ass." A woman hissed. A man answered.

"It's not Raphael we need to worry about. He doesn't run this place."

"Bu-" A hand touched Clary on the shoulder and she jumped in surprise pointing her weapon at a raggid Isabelle. Her right sleeve was torn from the shoulder and dirt covered one ride of her face. She put a finger to her lips before pointing at the ceiling. Something had definitely happened. Whatever it was wasn't good. Clary followed Isabelle away from the door.

"We got ambushed the second we came in." She whispered so quietly a normal Shadowhunter wouldn't have been able to hear her easily. "Jace and Alec are upstairs… How'd you get in here? The back doors were locked." Clary shrugged.

"One was unlocked." Isabelle blinked but shook off her confusion. "Is this the only way up?" Isabelle shook her head. She led Clary back through the kitchen and passed the door she'd entered from before coming to an open freight elevator shaft. Looking down Clary could see the car a floor down. They had to climb the cables.

Clary pulled one hard, but it stayed intact. "They're on the fifth floor." Clary blinked. They were currently on the second based on where the car was. She assumed there was a basement. She climbed the cables effortlessly while Isabelle straggled behind. She had to wait for her on the edge of the metal doors.

"Can we kill them?" A man asked. There was a smack.

"Do you want to break the Accords?" Another man with a Hispanic accent snapped. "No. We don't kill Shadowhunters. Muy Stupid."

"You're the stupid one." Alec snapped. "Holding us captive? I don't think the Clave will respect this."

"You came onto _my_ property. I have the right to protect my clan." Isabelle joined Clary on the ledge holding on for dear life.

"Not when you kidnap mundanes." The man laughed.

"Right." Clary had never been in an elevator. She had no idea how heavy the doors were but she was ready to throw them open. She looked at Isabelle who nodded in agreement before Clary slid open the door and wielded her Seraph Blade. Alec was bound to his knees with his hands behind his back. Jace was slumped on the floor unconscious.

The vampire before them was tall and slim with olive tinted skin that matched his accent.

"I don't think we've met." The vampire said smiling. When Clary didn't respond he frowned. "I was wondering when you'd make an appearance." He added referencing Isabelle.

"Give us the Mundanes and we'll leave." Isabelle snapped back. "We aren't here to pick a fight."

"Could've fooled me." Two Vampires, both female appeared from the doorway behind Alec.

"Raphael this is ridiculous. What is the point to all of this?" Raphael studied Izzy with wandering eyes before responding.

"What is rediculoso is that my clan's leader decided it was a good idea to get them addicted to cocaine. Do you understand that? I don't. I'm left to deal with the madness. You were not permitted onto this property. So I will do as I please." He nodded at the females who came running at them. Isabelle readied her whip as Clary pulled her seraph blade killing the blonde in a matter of seconds as well as the redhead gunning towards Isabelle.

"Was that a joke?" Clary asked. Raphael was silent. Isabelle's whip wrapped around his neck throwing the vampire to the ground hard. He hissed. Clary untied Alec's hands and feet. "Glad you left me outside?" She snapped at him. Alec only grimaced.

Distracted they were unaware of a vampire grabbing a groggy Jace. Clary spun on her heals and grabbed a throwing star from her belt, whipping it at the vampire's head. This knocked the thing backwards and caused it to lose it's grip on Jace. Alec killed it. Clary caught Jace as he fell and shook him.

"Jace. Wake up." He rubbed his face with his hand and yawned. When she was sure he could stand on his own she let go only to see Alec staring at her. Raphael was struggling to get free of the whip.

"Where are the mundanes?" Alec yelled at him. Raphael only sighed.

"Dead. Most likely. Each one I catch with a mundane I punish but not before the mundane gets drained. I told you. It's the addiction-"

"That would make sense." Alec snapped. "If one of them weren't a normal high school student." Raphael snorted.

"Probably not normal then." The whip tightened on his neck. "They would be in the basement with my clan." He finally said. "They will not touch Valentine's Daughter." Alec glanced at Clary. "You see, they aren't a huge fans of demons."

 **R &R!**

 **-Jen**


	14. Chapter 14

**My computer died. I saved this chapter before. Still lost it. I have no idea what happened. -_- I HAD 1800 WORDS. What I did was summarize what I had previously written. I think it still turned out okay.**

 **R &R**

 **-Jen**

 **Ch. 14**

Jonathan ran his hand along the wall of Clary's bedroom as he paced, glancing out the window occasionally. Not once since she'd arrived at the Institute had she physically left. She was always right where Jonathan could reach her if need be. But to his astonishment as he teleported in that evening she was gone and he was forced to wait for her. He restrained himself from going through her sketchbooks knowing it would only make him angry. He didn't want to be angry. It would ruin his night.

It was almost six when he heard her voice. "Jace," Clary's voice echoed from the other side of her door. She sounded both tired and annoyed. "please get some rest." He kissed her. Jonathan felt every muscle in his body tense. "Yes, I'll be at dinner." She turned the door knob.

As they group walked back to the Institute, Clary held her breath. Being called a Demon was not an everyday occurrence. It was Jonathan who normally got awarded that title. However the farther they walked the calmer she became. Noone cared what a vampire said. No one noticed her tense and no one called her out. Even after being sent into the basement to find the mundanes. Raphael had said the clan wouldn't touch a demon. However he could communicate with them telepathically and he could've easily ordered them not to touch her. The one mundane who'd still been alive had been a lost cause. He'd been fed vampire blood was already a changeling.

"Please," He'd whispered grabbing Clary's wrist. She'd been busy studying the other corpses. "help me." She'd shaken the poor guy off and left promptly.

Jace was limping. Though it wasn't much and no one seemed to be paying him much mind. "Are you okay?" She asked quietly. He pulled her into him, wrapping an arm around her casually. Nonchalantly, he was using her as a crutch.

"Peachy." He muttered. They dispersed once inside the Institute, Alec off to talk to Jocelyn, and Isabelle to take a shower. Clary helped Jace up the steps but stopped short of her room.

"Will you come with me?" Jace asked. Clary frowned.

"Jace, I can't. Just get some rest." He sighed running a hand through his hair.

"Will you be at dinner at least? I'm worried about you. What happened in that basement?" She studied his longing eyes and after a minute nodded ignoring the last question.

"Yes, I'll be at dinner." She said forcing a smile. He leant in and kissed her before shuffling to his room. Shaking her head she opened the door to her room and stepped in shutting it behind her.

"Hello Clarissa." She jumped, thinking at first that it was her father. It was only Jonathan, lying comfortably in her bed. She narrowed her eyes.

"What the _fuck_ Jonathan?" She seethed. He grimaced.

"What a wonderful way to greet your brother." He snapped back. "Every single time. We need to work on your sensory awareness." Clary was silent. Jonathan stood up from the bed. "Would you rather I teleport into your bathroom and knock? You could be in there taking a shower." He paused, cocking his head to the side. "Now that I think of it…"

"Jon." Clary huffed. He shrugged.

"It doesn't matter anyhow. Father's coming tonight." Clary turned to her dresser, thinking. Jonathan walked over to her but didn't touch her. "You get to come home." When she didn't speak he sighed. "Clary-"

"When?" She asked softly. He caressed her arms.

"Late. Hopefully when everyone's sleeping." Clary snorted.

"I thought father liked big entrances."

"I asked him the same thing. He told me to get out."

"I'll be ready." Her voice was soft and Jonathan noted a hint of sadness.

"Do you want to stay here?" He snapped, spinning his sister around to face him.

"No, I-"

"You want to stay here with out pathetic excuse for a mother and her halfbreed? Clar-" She stood on her toes and kissed him cupping his cheek with her right hand. It was meant to be a quick kiss to calm him down but he placed his hand behind her head, locking her in and deepening the kiss. Clary let him. Finally she pushed away from him and moved to the window, holding herself. Jonathan stared at her. For a moment all was calm. "Did you think I didn't know." He asked softly, not approaching her again. She tensed. "Have you fucked him?" Clary closed her eyes, tears threatening to spill. Though his statement was random it was very much Jonathan.

"No." She answered.

"Good." He snapped. "Because nothing would've stopped me from ripping head from his body."

"Jon," She said quietly.

"We will discuss it when you are home. Do not test me Clary." When she turned around he was gone.

"Clary?' It was late, almost ten when Jace found her in the training room beating up a punching bag. She didn't look at him. "You weren't at dinner. I knocked on your door-"

"Sorry." She answered absently. He went to touch her shoulder but she moved away, continuing to hit the bag.

"Are you okay?" Clary stopped her punching. Her eyes were red. "Have you been crying?" Clary sniffed.

"No." She mumbled. She didn't cry. If Valentine could see her… "You should just go Jace." She added. He stood there confused.

"Just this morning we were making out and tonight you want to give me the cold shoulder?" He took both of her hands in his. "What's wrong?" She worked her jaw back and forth.

"it's a long story." She finally said, moving to sit down.

"How long have you been in here?" He asked.

"What time is it?" Jace worked his jaw.

"Almost ten."

"a few hours."

"Just beating up the punching bag? What did it ever to do to you?" Clary smiled sheepishly.

"Funny," she said leaning into him. They sat there listening to creak of the metal that held the bag as it swung back and forth. "I'm scared Jace." She said finally. "I've never been scared before." Jace played with her fingers in his hand. They were so tiny, young, yet calloused from years of training.

"What's there to be afraid of when you've got me?" Clary looked at him and sighed.

"That's what I'm afraid of." She said honestly, her voice so soft he barely heard her.

"I love you Clary." Jace said, kissing her temple. She didn't return the remark.

It was midnight. Clary walked into the kitchen, wearing sweats and a lose tshirt. Underneath though, she wore tight leather pants and her combat boots. She was tired but knew the second she decided to sleep her brother would wake her up.

"What're you doing Clary?" She jumped sky high. Jonathan had been right. She needed to work on her sensory awareness. Sitting at the kitchen table was Alec, wearing only loose pants.

"What's it to you?" She snapped back pulling out a glass and pouring herself some water.

"I don't trust you." He said.

"I had no idea." Turning on her heels, she left him alone in the dark, and went back upstairs, stopping at the mystery door. She placed her hand on it and listened. Someone was inside. Taking a deep breath she knocked. No more than a minute later the door swung open, exposing Jocelyn in the same clothes she'd been wearing that morning.

"Clary!" She said, surprised. "What are you doing up?" Clary shrugged. If she could only get in that room... She just wanted to _look_ before her family got there.

"I couldn't sleep." She answered. "Are you busy?" Jocelyn raised her eyebrows.

"Uh, no not really." She glanced down the hallway. "Come in." She stepped aside, watching her carefully as Clary stepped across the threshold. Inside the room were two bookcases behind the large oak desk. Against the window was a comfortable looking brown couch. There were only two paintings on the wall of the office and neither had a cup. An easel was placed against the far wall. "Like what you see?" Jocelyn asked sitting at her desk. Clary turned to her.

"It reminds me of Father's study." Jocelyn shrugged.

"We did have some of the same tastes. I didn't just marry him for his looks." Clary snorted.

"Thanks for uh, letting me go with them today." Clary said. "I really needed to get out." Jocelyn nodded slightly shocked by her gratitude.

"I know you did." Silence. She needed to think. What could they talk about that wouldn't make Jocelyn suspicious?

"I don't feel safe here anymore." She said slowly. "Not that I ever really did but something just seems… off." Jocelyn took a deep breath. She looked around her office before speaking.

"You've felt that way too?"

"I've been dreaming. Seeing things. I think they might've found me." Jocelyn shook her head at the statement.

"Impossible Clary. Magnus hasn't picked up on any of the Circle members in New York City." He hadn't picked up on Jonathan. The all powerful warlock should be more observant.

"I'm just worried is all." Clary muttered. Jocelyn stood.

"Maybe you need sleep. I heard you were in the training room for hours tonight. Your body needs to rest sometime." Clary stood. Jocelyn opened the door.

"Hello Mother." Jonathan said. All Clary heard was a gasp before Jocelyn was knocked backward into the room, hitting her head on the side of her desk. Jonathan tried to step forward but hissed, drawing back. Jocelyn groaned on the floor.

"Out of the way Jonathan." Valentine snapped, moving his son out of Clary's view and stepping over the threshold. Bending down he touched Jocelyn's shoulder, checking her for any wounds. Satisfied, he drew a rune on her bare skin. "She shouldn't be waking any time soon." He turned to Clary. "Clarissa." He said in greeting. She nodded.

"Father."

"Why can't I enter?" Jonathan snapped, standing in the doorway. Valentine turned to look at his eldest son.

"Its probably protected from Demons." He answered. "Where's the cup Clary?" She shook her head.

"It's not here father." Jonathan growled.

" _Clary,"_ She glared at him.

"There's only two other places it could be." She answered her father.

"Alec is awake." Clary told them as they made their way to Jocelyn's bedroom. Jonathan had his Seraph Blade out already but he nodded to her in thanks for the information. Clary opened the door with a creak and slipped into the large bedroom, flipping on the light switch. The paintings she'd seen before were all still there, hanging neatly on the wall. She hadn't paid much mind to them the last time she'd been in the room. Back then they'd just been paintings with no real significance. In fact it was too easy to find the cup, in the painting above the couch. Clary pulled it down, examining it. On the back of the frame it said "Carpe Diem." _Sieze the day._ Hesitantly, Clary reached her hand into the painting until she gripped a hilt. It came out shining, lighting up Clary's eyes. Valentine snatched it from her hands, lifting it up to examine it. He was smiling. Clary moved over to Jonathan, feeling him wrap a hand around her arm, keeping her with him tight.

"We've got it." Valentine said in almost a whisper, a laugh escaping from his lips. "Now I can finish what I started." He glanced at his children. "Come. I have much to do." Jonathan shook his head.

"Father you promised." He said. Clary'd been out of the loop for months. She was lost in their conversation.

"Jonathan I have never promised you anything. He can be dealt with later."

"What's later?" Valentine narrowed his eyes.

"Come. Now." His words, cool and harsh cut throughout the air like a knife. Valentine grabbed a growling Jonathan, and together, the three of them teleported to their old home.

 **Too fast? Too Slow? Let me know R &R**

 **Lots of love**

 **-Jen**


	15. Chapter 15

**I love .com If I can't remember something all I have to do is look it up on the website. Makes life easier.**

 **The first half of this chapter is what Clary goes through when she gets back home throughout a matter of weeks. It's kind of like a montage.**

 **R &R**

 **-Jen**

 **Because I did the math, Clary was at the Institute for 10 months 1 week and 2 days.**

 **C: 15**

 **J: 17**

 **Ch 15**

For a moment after landing Clary felt calm. She was back at home with her family. However, there was no happy reunion. Jonathan wouldn't release his hand from her arm.

Valentine placed the cup in his safe, located in his study before spinning on Clary, slapping her right across the face. Losing her balance and in shock she fell back into Jonathan's chest. She kept her face neutral but her body was shaking involuntarily.

"Father-"

"Clarissa, please shut up." She bit her tongue. This was not normal behavior for Valentine. He'd always been careful around her brother as he was so over protective. However, it seemed at this moment that him and Jonathan were on the same page. They were both angry. Valentine took Clary's Chin in his hands and forcefully turned her head to look at him. He was not smiling. "Did you or did you not get involved with Jace?" She swallowed.

"Father-" Jonathan's hands tightened on her arms. "Jon you're hurting me."

"Clarissa." Valentine snapped.

"Yes." She whispered. What was the point in lying? Jonathan had already called her out the other day. Valentine stood straight. "It was a stupid thing. It wasn't serious-"

"Oh really?" Valentine snapped. "Because I talked with Starkweather. According to him, it wasn't a _little thing."_ Clary gulped. She'd forgotten about him. Hodge was good at being invisible. " _Make-out sessions in the library."_

"Can I please go back and kill him?" Jonathan asked through clenched teeth.

"No." Clary moved her eyes to the floor. She was tired and all she wanted to do was sleep. Though it was the middle of the day here, back in New York it was bedtime. "If I give you a job I expect you to do it. _Not_ get yourself a boyfriend!"

"It was a mistake!" Clary exclaimed. "It was a stupid mistake that should never have happened! I apologize!"

"Clary," Jonathan's voice woke her up from her dreams the next morning. Groaning she peeled her eyes open, and turned her head to look at her brother inches from her face. "Father wants you downstairs." Clary closed her eyes. Sighing, Jonathan removed her covers. Dried blood could be seen through the bandages on her back. "These need to be cleaned." He muttered.

"Go away Jon." She mumbled.

"I thought you wanted me? As I recall you couldn't stop screaming my name last night. That was nice." A tear slid down Clary's cheek as she recalled the whipping Valentine had dealt her in front of her brother. Knowing Jonathan was her protector, she'd wanted his protection: This, especially because Valentine had gone above and beyond her usual punishment of five. Valentine had done a lot of work on Clary's back. There had been a point when she'd passed out but Jonathan had been ordered to hold her up. There was even a whip scar that reached under her ear to he corner of her chin from when she'd fallen, almost resembling a red colored rune. "Father was pissed." He muttered

"You were too." Jonathan snorted, peeling over the bandages. Clary cried out.

"Was? I am. You need to learn to listen Clary. To me. To Father. You're _mine."_

 ** _2 weeks later_**

Clary was silent. With a blindfold over her eyes, she couldn't see a thing. "Sensory Awareness" as Jonathan called it, was important. She knew she was standing in the middle of the training room because that was where Jonathan had left her. They'd been doing this on and off for the last week and a half. Ninety percent of the time had just been Jonathan knocking her over.

And over.

And over again.

She was finally getting the hang of it. Jonathan was to her right, walking silently passed her. That was the thing with Jonathan: He was deadly silent. He was proud of it. However, the training had paid off and she could finally pick up the quiet footsteps that were his. He came at her and she backed up making him rush passed her. It wasn't over though. Hearing him was one thing. It was another to dodge a silent weapon like a Seraph Blade. Listening for the whistle of the practice stick, she ducked, rolling to her right. "Not bad." Jonathan said pulling the blindfold off her head. She blinked, black spots dancing across her vision. "Two hours and I knocked you down ten times. Better."

"Jonathan. My office." Valentine said, walking towards his study. Grumbling to himself Jonathan put the stick away and followed his father.

"Wait for me in your room." Jonathan had become much more restricting with Clary. He rarely let her out of his sight. She didn't argue with him. There was no point.

"I need the Mortal Sword." Valentine said once Jonathan had shut the door. He wasn't surprised.

"It's in the Silent City." Jonathan said. "How do you expect us to get it?"

"You and Clarissa." Valentine added as if it were obvious. "It shouldn't be too hard with her abilities." Jonathan sighed.

"She hasn't been all that helpful recently." Valentine agreed.

"She will be." Jonathan narrowed his eyes.

"What are you going to do?"

"It's what I planned to do even before she started whoring around with Jonathan." _Jace._

"What?" He asked with a bite.

"Just get me the sword Jonathan." Valentine sighed. "Don't worry about it." Jonathan didn't like it. He went up to Clary's bedroom and opened it without knocking. She was curled up on the window seat staring outside.

"What did Father want?" She asked.

"We're going to die. Plain and simple." Clary muttered as they ventured through The New York Marble Cemetery at three in the morning. They were both dressed in black shadowhunter's gear, with Clary's hair hidden by a hood connected to her leather jacket. An owl cood from somewhere in the creepy looking trees.

"You practiced those runes. As long as you use them we'll be fine." They came to a large angel statue holding a replica of the mortal cup. Jonathan withdrew a vial from his jacket pocket and poured the substance into the cup. Worried that Jonathan and Clary's blood was too tainted, Valentine had provided a vial of his own, as it was the key to entering the Silent City. There was a creaking as the ground shifted to reveal a staircase under the statue.

The two siblings readied their Seraph Blades as they descended into the darkness. As they reached the bottom of the steps, a blast of wind blew back Clary's hood, revealing her hair. She'd never been in the City of Bones before. The place was massive. "This way." Jonathan knew where he was going. According to Valentine, he'd been at the chamber once or twice back when he was appreciated. He'd drilled the directions into Jonathan's head. They turned right down a small corridor lit by faint torches hanging on the walls. Together they moved silently and swiftly.

After winding and turning for five minutes they came to their first Silent Brother. He turned to them and began to speak but Clary cut him off with a quick cut to the head, killing him instantly. She didn't have a chance to study the sewn mouth of him and the old calloused skin as Jonathan had moved on. She jogged to keep up with him.

The council chamber had about ten people in it, filled with various shadowhunter's but more Silent Brothers than anything. Jonathan gave her the signal and with a quick glance, she withdrew her Seraph Blade, and pulled out her Stele. She sketched a quick rune on the structure and moved away quickly, taking cover. The building shook, a large crack crawling its way up from the rune. Part of it collapsed and dust filled the passages. There was yelling. After the dust cleared a few of the Shadowhunters ran out. They weren't expecting any kind of attack. They were more confused than anything, but Jonathan killed them quickly and as quietly as possible. Leaving Jonathan to deal with the fight, Clary ducked into the Speaking Stars Pavillion, hoping that the Mortal Sword _,_ had fallen in the collapse.

It was beautiful to Clary's eyes. It had a double-edged blade with outspread wings emerging from the hilt. She knelt, removing her backpack from her shoulder, and took out a blanket. Holding the sword was said to cause some kind of pain. Valentine said a blanket would help. Clary knew better than to question him.

 _"Clarissa Morgenstern."_ The voice entered her mind. Laying on the ground, trapped by debris was a Silent Brother, staring at her. She couldn't tell if he was in pain as his face was sewn. She turned back to the sword, hanging loosely near the center of the room. _"Do not take the Soul-Sword. It will destroy this world."_ Clary could feel him picking away the thoughts in her mind. She moved quickly, using the blanket to pull the heavy sword down from its post. She tied it down and placed it in her backpack. _"I beg of you don't-"_

"Shut up." She snapped at him, fitting half of the sword into her backpack and zipping it. It made the thing easier to carry. "Jon!" She yelled. "Lets go!" She drew her portal rune on the floor. Jonathan jumped over the debris and came running, grabbing her wrist as he ran into the portal, pulling Clary with him.

Valentine took the backpack from Clary, not bothering to remove the sword and walked back into the house. "No thank you I suppose." Clary muttered, following Jonathan into the house to the kitchen.

"There's still more to do." Valentine said once the sword had been put away. Clary's hair was a dusty brown color from the raining of debris. Her face was coated with it as well. All she wanted was a shower.

"What do you need Father?" Jonathan asked, standing at attention. Clary wasn't prepared for what she heard.

"The ritual I want to preform requires the blood of four downworlder youths. Vampire, Fey, warlock, and werewolf." Clary tensed but stayed silent. She knew better than to speak out against her father. "I have a large cargo ship in the New York Harbor. Bring them there alive."

"Where did you get a cargo ship?" Jonathan asked.

"Does it matter?" No. It really didn't.

Clary woke up to Jonathan sliding under her sheets. He'd stopped asking for permission to sleep with her. Now, he just did it regularly. Clary turned to him in the dark, stretching.

"Jon?" She mumbled as he pulled her into his arms.

"Shh, go back to sleep Clar." He whispered, kissing her forehead. She looked up at him.

"What time is it?" He yawned.

"4am." Clary had gone to bed around ten that night. She would be getting up in two hours to make breakfast. Her conclusion was that Jonathan had been in his own room. He just woke up and decided to move in with her.

"Is Father crazy?" The words slipped out of her mouth before she could stop them. She'd been thinking about it all day. Valentine had secret plans but he confided in his son. Jonathan was silent for a moment.

"Yes." He answered plainly. "But we need to do what he says." Clary closed her eyes, pressing her head into Jonathan's chest.

"Why?" Jonathan sighed. The truth was that Jonathan had his own plans but in order to go through with them, he needed Valentine to do some of the work.

"Just go to sleep Clary."

 **I hope you guys liked this I'm 50/50.**

 ** _PLEAAAAAAASE_** **let me know what you thought**

 **R &R**

 **-Jen**


	16. Chapter 16

**This is a really long chapter. I had so much fun writing it.**

 **-Jen**

 **Ch. 16**

"I missed this." Clary said, closing her eyes and taking in the smell of blood in the air. Jonathan smiled at her as she did so, kicking the body over. Valentine had been worried about Clary's behavior. His solution had been to give Jonathan and his sister some free time. This included killing, which also included the chase- something Clary had never really taken part in. They hadn't left Idris; in fact, they only traveled a hundred miles to find downworlders.

"I missed you." Jonathan said. It had been a long time since he'd seen her smile as she was.

"How long did father say we had?"

"The day." He answered. "Which is about over. We should head back." Clary sighed. "I know." He kissed her forehead and pulled her close.

"I like this place."

"You won't once the wolves find their dead pack member. Come on." She drew the rune and together they traveled back to their home.

Valentine was not there when they returned. While Jonathan took a shower, Clary took to making dinner. She decided on Chicken and broccoli. The siblings ate quietly together. Valentine didn't make an appearance until eight thirty.

"Clarissa, Jonathan," He said nodding to them in greeting.

"Father." They said together from the living room. Both siblings sat on the couch, reading their own books. Clary's legs were on Jonathan's lap.

"Good trip?" Clary smiled. "Good." He promptly left to his study. That night, Clary slept alone in her bed happy and content. The next morning though was another story.

"Do I get to kill him?" Jonathan asked, a smile forming on his lips. Clary glanced at him. Her arms were wrapped around herself as she listened to her father give them instructions for the day.

"No, Jonathan." Valentine bit back. "Clarissa, you don't look too happy." Clary glanced up at him and her brother.

"No." She lied. "I'm fine." Valentine stared at her. She stared back. "Why do you want Jace anyway?" She sighed.

"If you were listening," Valentine snapped. "You would've heard me say that I want him because _I can have him."_ Valentine sighed. "Jace is a lost soul, whom I raised. It will not be that hard to manipulate him."

"Into what?" Jonathan asked, adding to the conversation. "You threw him away years ago, because he was too soft." Valentine smiled.

"If that's what you want to call it." He said. Clary rolled her eyes. She had a feeling that he wasn't only trying to manipulate Jace. He was trying to manipulate her as well. Together they teleported to the cargo ship. It was pretty huge. Valentine led his children to the Captain's quarters. Clary shrugged off her favorite jacket and threw it on a chair.

"If you're ripping up my clothes you aren't touching the jacket." She told Jonathan, who only smiled at the prospect. "Is this another form of punishment?" She asked once Valentine had excused himself to the lower decks where the downworlders were being kept.

"Beating you up or having you talk to Jonathan?" Jonathan asked sounding bored as he rolled up his sleeves.

"Jace." She answered.

"Probably." He answered. "If you can convince him you're biological siblings he might be more sympathetic."

"We aren't. And I don't want to tell him that." Jonathan shrugged and without warning slammed his fist into Clary's left cheek knocking her into the table in the center of the room. Before she could respond, he grabbed her roughly by the arm and threw her into the glass wall facing the New York harbor.

"Fuck Jonathan!" She cried out when he gave her a minute to breathe. A bruise was already forming on her cheek. Jonathan bent down and pulled Clary's Stele out of her boot and tucked it into his back pocket.

"Thanks for giving me the motivation to beat you up." He said smiling. Clary glared at him. "You told us you felt it was a mistake getting involved with him."

"It was."

"Yes. But you still _want_ to be with him." Clary closed her eyes.

"No."

"Don't lie to me." She ground her teeth. "You are mine Clary."

"And if Father knew about your sick perverted thoughts?" She asked softly, making Jonathan turn on her.

"I'm a demon Clary." He bit out. "I do what I shouldn't. He knows how I feel about you." With that, he stormed off. Hearing a click, Clary ran to the door and tried the handle. The bastard had actually locked her in the room.

Jonathan stood outside of the Institute. The air was cool and humid, as if it were to rain. He needed to get to Jace and he considered teleporting into his room. The issue was that he wasn't a hundred percent sure where the room was the Institute. It wasn't safe to teleport if you didn't know exactly where you were going. He could do the other thing… Shaking his head, he pulled out Clary's phone. Jocelyn had given it to her in case there was an emergency. He wasn't even sure if it still worked. However, Clary hadn't even been gone an entire month yet. The chance that it was deactivated, or that it was on the top of Jocelyn's to-list, was slim. After a little bit of stumbling-Jonathan had no clue how to work a phone- he found a contact titled Jace. He put the device up to his ear and waited.

"Clary?" The voice sounded on the other end of the line. Jonathan smiled.

"Think again." He said, sounding very Maniacal.

"Who is this?"

"Clarissa's big brother." Jonathan answered. "And if you want to see her alive again, you'll meet me." Jace was silent on the other side. He waited.

"Where?" Jonathan frowned. He really did care for Clary. That wasn't good at all.

"Third Street Ally. Fifteen minutes." He paused. "Oh and Jonathan? Come alone."

Jonathan waited on the roof of a nearby building. If anyone else came out with Jace he'd smell them. Jace stopped just outside of the ally, refusing to enter. It was narrow and easy to be ambushed. He pulled out his Seraph Blade.

"That won't help you." Jonathan said jumping down. Jace narrowed his eyes.

"Where's Clary?" Jonathan sighed.

"Right to the point I see." He muttered. Faster than lightening, Jonathan knocked the blade out of Jace's hand and pinned him to the brick wall. "You literally walked out here by yourself. Because I asked you to?" Jonathan laughed. "How stupid are you?"

"I'm worried about Clary." Was his simple answer. Jonathan shook his head.

"Didn't Father ever tell you that to love is to destroy?" Keeping a firm hand on Jace, he twisted the ring on his finger, taking Jace to the ship.

Jace woke up in a cell located in a small room that held a desk and instruments- not the musical kind. It was dimly lit. He rubbed his head slowly, trying to make sense of what had transpired only hours earlier. Catching movement to his left, he shot up into a standing position, despite the throbbing pain that erupted in his brain. Clary slowly stepped into the light, keeping her distance but giving him enough visual.

"Clary?" He asked groggily?

"Hi Jace." She answered. Her voice was light and soft, unnatural to his ears.

"Where are we?" She shrugged, looking everywhere but directly at him.

"A ship." Her head shifted and he caught a glimpse of a bruise on her upper arm. It looked like a hand.

"What happened to you?"

"Father." She brushed back her hair, giving a clearer view to her cheek. "He was mad that I left… I didn't know they were bringing you here."

"He threatened to kill you." Clary sighed.

"Jonathan?" Jace's silent was enough. "Of course he did." She muttered. "Jonathan wouldn't kill me."

"Are you… free to walk around here?" Clary nodded.

"Only because there's nowhere to go." She laughed to herself. "We're on a ship, actually. The only way off would be to jump into the freezing waters and drown…" Jace studied her face. She could feel him searching and she could guess what.

"Jocelyn says you have the mortal cup-Valentine does. Alec thinks you helped willingly." Clary snorted.

"Of course he does." She looked at Jace, wrapping her arms around herself. "If I hadn't helped him, he would've killed me."

"You said Jonathan wouldn't."

"Valentine." She whispered. "He was furious when he found me." She sighed, shaking her head.

"And the Mortal Sword?" Her head shot up.

"I-I had to-"

"You killed people."

"How do you even know about that? Look it doesn't matter-"

"Your hair is a dead giveaway."

"I didn't have a choice." Jace narrowed his eyes.

"Everyone has a choice!" Clary turned away from him towards the door. She could hear Jonathan pacing outside. He didn't want her around Jace, especially alone. It would be better to wrap this up.

"You sound like Alec. Jace… I need to tell you something. You aren't going to like it." Jonathan stopped pacing. "We're related." Jace scrunched up his face.

"What are you talking about?"

"I didn't know until Father dragged me back here. He found out we had a … relationship. She just had to say it. "You're my brother Jace." He snorted.

"And I'm ugly." Clary restrained herself from laughing.

"I'm serious."

"Jocelyn isn't my mother."

"No. But Valentine's your father. Haven't you wondered why you're so much stronger than other shadowhunter's? I bet you could jump from a five story building and land without a problem." It was actually ten, but he wouldn't tell her that. "I wish I was lying." She said.

"We- we had sparks Clary." She closed her eyes. "I would know if we were related. I told you about my father. I told you how he died-"

"Have you ever seen a photo of Valentine? Have you ever seen his face?" Silence. "Then please don't get mad at me until you see him." Silence stretched in the small room. Jace worked his jaw and flexed his hands. Then finally he spoke but it wasn't what she'd been expecting.

"Do you remember that day you were sick?" He asked quietly. Clary tensed. "I was there _all day_ making sure you were okay. I-" Clary could just feel Jonathan snap on the other side of the door and knew without a doubt that he'd lost his restraint. He stormed in, getting into Clary's personal space.

"You were sick?" He snapped. Jace looked between the two siblings, perplexed.

"Jon-"

"Clary. Were you having pain?" She pursed her lips, and stared at Jace, her face void of emotion. "Clarissa!"

"Don't tell Father." She answered urgently. "Please, Jonathan. I don't want him testing my blood again!"

"What's going on?" Jace asked. Jonathan's head snapped towards Jace. He took a step towards him.

"Jon, don't." Clary said grabbing his arm He shook her off.

"You want to know what's _going on?"_ He snapped. "I don't like you. I have never liked you. You're like this fly that I just can't _kill._ " Jace was silent.

"Father will be mad-"

"He's not here." Jonathan said. "As I was saying…when I do find a way to kill you it will be slow. And painful." He took a few deliberate steps towards the cage.

"What did I ever do to you?" Jace asked. "I don't even know you."

"Jonathan." Clary warned. He was too far-gone to notice. He laughed. Jonathan Morgenstern laughed and it chilled Clary.

"You don't have to know me. I know you. Oh I _know_ you. Precious little Angel Boy. Grew up to play piano and have the relationships _I_ wanted. I only ever wanted someone to be there for me. I did. I had Clary. And you got _Father._ " He wrapped his hands around the bars. "Oh and then Father decided to send Clary right into your fucking arms." Clary gulped. Quickly, she grabbed Jonathan's arm again.

"Jonathan look at me." It was the only way to get his demon to calm down. He needed to see her. Look at her. Feel her. But Jonathan was ignoring her. Too focused on his enemy.

"He sent her to the institute to get the mortal cup. And _you_ had to be there.' Jace looked at Clary. She felt the blood drain from her face. She'd wanted to hide that from Jace. She really did like him.

"Jace I'm sorry." Clary whispered. "I never wanted this to happen. I never wanted any of this to happen." Jonathan looked at her then. Clary looked back. As he spoke he kept his eyes trained on his sister.

"Father ordered her to get close to you. She never loved you." Jonathan had lied. Clary looked between a heart-stricken Jace and her brother. She'd been punched and whipped and thrown. She'd been lied to, deceived. She'd let herself be the victim. She saw red.

"What. The. FUCK. JONATHAN!" She shoved him hard, knocking him backwards until he hit the wall. She kept hitting him.

"Who's holding who against the wall now." Jonathan purred. Clary punched him hard enough to illicit a groan. Jonathan caught her next punch, and spun her around so she faced Jace, wrapping his arms around her waist. "Calm down little sister."

"You're telling me to calm down!?" Clary yelled.

"Jonathan Christopher Morgenstern." Valentine's cold voice cut through the room. Clary immediately stilled, dropping to her knees. Jonathan released her, standing straight. Jace was also still as a statue. Staring with wide eyes at the man who should've been dead. "What is going on here?" Valentine practically seethed, stepping into the room.

"Making things abundantly clear to Jace here." Jonathan responded. "Clary lost her shit."

"Language." Jonathan shrugged. "Clarissa get up." She did as she was told. Keeping her eyes straight ahead. Valentine grabbed Clary by the arm and dragged her outside. "Jonathan, come!" Like a dog, he yanked her up the steps to the room on the top floor. "You had one job- one thing to do. And you couldn't even do that." Valentine seethed.

"Jonathan-"

"I don't care what Jonathan did. You were responsible and now I have a mess to clean up." He threw Clary into the spacious room. She lost her balance and fell on all fours.

"Dad-"

"I don't want to hear it." He slammed the door shut, locking it, and leaving Clary to her own thoughts. After a moment of silence, she did the only thing that would help her calm down. Like Jonathan, she broke stuff.

Jonathan felt partially guilty for allowing his father to hurt Clary. But she'd hurt _him._ She'd betrayed _him._ Shaking his head Jonathan turned from the railing to look up at the captain's quarters. Clary was up there having some sort of meltdown. With his hearing he could make out his sister complaining loudly to herself. Jonathan took the metal steps up and unlocked the door.

"Clary," Jonathan said. She stood on the opposite side of the room, staring out the glass wall at the view of New York City's shoreline. She was dressed in her combat gear, including her favorite leather jacket. Her arms were wrapped around herself as she stared.

"What do you want Jon?" She snapped.

"Are you okay-" She turned.

"Do I look okay Jon? Do I _sound_ okay?" Jonathan was silent. "Because I don't _feel_ okay." He approached her slowly. "I want my Stele back."

"Not happening."

"Jon-"

"Clary, No." His voice was hard. Clary stared at him, anger evident in her eyes. "You need to calm down." She shook her head.

"Just get out." Jonathan sighed. He thought about telling her that she couldn't tell him what to do. Telling her that she had to do what _he_ said. But he didn't. Instead he slammed the door shut, locking it before heading down to find his father. He wasn't waiting any longer.

Jonathan entered the cargo hold, striding past the caged downworlders screaming his death, and to the back room. Valentine stood hunched over a desk, as he normally did in the basement of their house. He was reading the old book Jonathan had brought him months ago.

Jonathan didn't acknowledge his father, but instead went to the small wall height cage in the corner. He hit the metal with force, shocking Jace into backing up.

"Jonathan, leave him alone." Valentine said sounding bored. Jonathan snarled.

"How about one cut to his pretty little face?" Valentine didn't respond. There wasn't a need to.

"I like my pretty face thank you." Jace snapped back. Jonathan cocked his head to the side a grimace on his face. "Yours could use some work though." Jonathan pulled a knife from his belt. Reaching through the bars he grabbed Jace by the collar of his shirt and pulled him forward, pointing the knife at his throat.

"Thin skin Jonathan?" Valentine muttered. He still didn't bother looking up.

"Do you know how long I've had to wait to get my hands on you?" Jonathan growled. Jace snorted.

"Sorry to disappoint. I'm not into dudes." Valentine sighed as Jonathan opened his mouth to speak.

"Come here." Jonathan pushed Jace backward into the wall hard enough to hurt, and turned towards his father.

"Why won't you let me play?" He asked.

"If I were to let you _play_ with Jonathan, he would be dead." Jonathan smiled.

"I have some self control Father." Valentine looked up.

"No. You do not."

 **This is the longest chapter I've ever written. I hope you guys liked it!**

 **I love suggestions for the next chapters!**

 **R &R**

 **-Jen**


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